Saman, not Salman.
On 2/11/16 10:09 PM, Bill Ross wrote:
> Dear Salman,
>
> The crash suggests an amber14 bug in any case, possibly the sort that
> can be worked around with better coordinates, but maybe something for
> the developers to reproduce and study, since it is occurring when
> nonbonded lists are being adjusted, probably due to an index error. I
> don't think it's a problem with the files if the same ones worked with
> amber12.
>
> Bill
>
>
> On 2/11/16 9:41 PM, Saman Yousuf ali wrote:
>> Dear Ross,Thanks for your prompt response. I understand your point but my question is that why amber12 run complete minimization without any error and remove all bad contacts. I have pasted amber 12 restraint minimization step below,
>>
>>> Minimization Amber12
>> &cntrl
>> imin=1, maxcyc=1000, ntmin = 2,
>> ntx = 1, ntc = 1, ntf = 1,
>> ntb = 1, ntp = 0, ncyc = 100,
>> ntwx = 1000, ntwe = 0, ntpr = 1000,
>> ntr = 1, cut = 10.0
>> &end
>> Restraints
>> 25.0
>> RES 1 541
>> END
>> END
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 1 2.4609E+10 4.7180E+09 1.1524E+12 HH22 8003
>>
>> BOND = 496.9463 ANGLE = 2333.9871 DIHED = 6282.8322
>> VDWAALS = ************* EEL = -153221.8685 HBOND = 0.0000
>> 1-4 VDW = 4003.3299 1-4 EEL = 23949.5332 RESTRAINT = 0.0000
>>
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 1000 -1.4952E+05 4.5138E-01 9.1652E+01 CD 7737
>>
>> BOND = 10115.2618 ANGLE = 1331.2640 DIHED = 6321.1470
>> VDWAALS = 19411.8908 EEL = -213616.7315 HBOND = 0.0000
>> 1-4 VDW = 2342.1151 1-4 EEL = 23166.8032 RESTRAINT = 1405.2656
>> EAMBER = -150928.2495
>>
>>
>> Maximum number of minimization cycles reached.
>>
>>
>> FINAL RESULTS
>>
>>
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 1000 -1.4952E+05 4.5138E-01 9.1652E+01 CD 7737
>>
>> BOND = 10115.2618 ANGLE = 1331.2640 DIHED = 6321.1470
>> VDWAALS = 19411.8908 EEL = -213616.7315 HBOND = 0.0000
>> 1-4 VDW = 2342.1151 1-4 EEL = 23166.8032 RESTRAINT = 1405.2656
>> EAMBER = -150928.2495
>> I have also run amber14 topology files with above minimization script then it works fine,
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 1 2.4609E+10 4.7180E+09 1.1524E+12 HH22 8003
>>
>> BOND = 496.9463 ANGLE = 2333.9871 DIHED = 6282.8322
>> VDWAALS = ************* EEL = -153221.8685 HBOND = 0.0000
>> 1-4 VDW = 4003.3299 1-4 EEL = 23949.5332 RESTRAINT = 0.0000
>>
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 1000 -1.4952E+05 4.5138E-01 9.1652E+01 CD 7737
>>
>> BOND = 10115.2618 ANGLE = 1331.2640 DIHED = 6321.1470
>> VDWAALS = 19411.8908 EEL = -213616.7315 HBOND = 0.0000
>> 1-4 VDW = 2342.1151 1-4 EEL = 23166.8032 RESTRAINT = 1405.2656
>> EAMBER = -150928.2495
>>
>>
>> Maximum number of minimization cycles reached.
>>
>>
>> FINAL RESULTS
>>
>>
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 1000 -1.4952E+05 4.5138E-01 9.1652E+01 CD 7737
>>
>> BOND = 10115.2618 ANGLE = 1331.2640 DIHED = 6321.1470
>> VDWAALS = 19411.8908 EEL = -213616.7315 HBOND = 0.0000
>> 1-4 VDW = 2342.1151 1-4 EEL = 23166.8032 RESTRAINT = 1405.2656
>> EAMBER = -150928.2495
>> I cant understand the reason of this error. I thought it is due to the minimization script which I have used previously for running minimization. The script is mentioned below.
>>
>>> AChE md_simulation
>> &cntrl
>> imin = 1,
>> maxcyc = 500,
>> ntpr = 5,
>> ntb = 1,
>> ntr = 1,
>> cut = 10.0
>> /
>> Hold the system fixed
>> 25.0
>> RES 1 541
>> END
>> END
>> Kindly tell me if there is any problem with this script.
>>
>> Thank you.
>>
>> Best Regards, Saman Yousuf AliJunior Research Fellow,
>> | Lab No. P-133, Computational Chemistry Laboratory
>> Dr. Panjwani Center for Molecular Medicine & Drug Research,
>> International Center for Chemical & Biological Sciences,
>> University of Karachi – 75270.Karachi-Pakistan.
>>
>> Contact No:
>> Office (92-21) 111222292 (Ext 309)
>> Email ID: saman.yousufali64.yahoo.com
>> saman.ali.iccs.edu
>>
>> |
>>
>>
>>
>> On Friday, February 12, 2016 10:19 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>
>>
>> Note that the atom with the GMAX is HH22, number 8003 for a few steps, then it switches to NE 7995 before the crash. I would look for steric clashes in the neighborhood of those 2 atoms.
>>
>> Bill
>>
>> On 2/11/16 9:14 PM, Saman Yousuf ali wrote:
>>
>> Dear Ross,
>> Thank you for your response. Few steps of amber14 minimization with ntpr=1 pasted below:
>> >NSTEP ENERGY RMS GMAX NAME NUMBER
>> 1 2.4609E+10 4.3599E+09 1.1524E+12 HH22 8003
>>
>> BOND = 497.0681 ANGLE = 2333.9871 DIHED = 6282.8322
>> VDWAALS = ************* EEL = -178499.9793 HBOND = 0.0000
>> 1-4 VDW = 4003.3299 1-4 EEL = 23949.5332 RESTRAINT = 0.0000
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 2 1.7440E+10 3.0014E+09 7.9330E+11 HH22 8003
>>
>> BOND = 497.0605 ANGLE = 2333.9938 DIHED = 6282.8328
>> VDWAALS = ************* EEL = -178489.9900 HBOND = 0.0000
>> 1-4 VDW = 4003.3332 1-4 EEL = 23949.5187 RESTRAINT = 0.0006
>> EAMBER = *************
>>
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 3 1.1686E+10 1.9440E+09 5.1381E+11 HH22 8003
>>
>> BOND = 497.0585 ANGLE = 2334.0055 DIHED = 6282.8336
>> VDWAALS = ************* EEL = -178478.7183 HBOND = 0.0000
>> 1-4 VDW = 4003.3373 1-4 EEL = 23949.5012 RESTRAINT = 0.0030
>> EAMBER = *************
>>
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 4 7.3545E+09 1.1758E+09 3.1079E+11 HH22 8003
>>
>> BOND = 497.0666 ANGLE = 2334.0249 DIHED = 6282.8350
>> VDWAALS = ************* EEL = -178466.1241 HBOND = 0.0000
>> 1-4 VDW = 4003.3425 1-4 EEL = 23949.4803 RESTRAINT = 0.0083
>> EAMBER = *************
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 16 1.8138E+07 4.7353E+05 9.6576E+07 NE 7995
>>
>> BOND = 501.8320 ANGLE = 2336.2317 DIHED = 6282.9787
>> VDWAALS = 18279092.5325 EEL = -178307.0467 HBOND = 0.0000
>> 1-4 VDW = 4003.5881 1-4 EEL = 23948.9560 RESTRAINT = 1.0630
>> EAMBER = 18137859.0723
>>
>> Sander runs for few cycles ( NSTEP 16 ) of minimization and stops with following error message (below).
>> Backtrace for this error:
>> #0 0x33E3419497
>> #1 0x33E3419ADE
>> #2 0x36184358EF
>> #3 0x4D5DB5 in nb_adjust_
>> #4 0x4D7FE6 in ewald_force_
>> #5 0x64AFCF in force_
>> #6 0x484743 in runmin_
>> #7 0x47132F in sander_
>> #8 0x46CBBC in MAIN__ at multisander.F90:?
>> Segmentation fault (core dumped)
>> But the same apo protein (with bad contact) via amber12 using ff99SB, minimization run perfectly with out any error message.
>> Thank you.
>> Best Regards, Saman Yousuf Ali Junior Research Fellow,
>> | Lab No. P-133, Computational Chemistry Laboratory
>> Dr. Panjwani Center for Molecular Medicine & Drug Research,
>> International Center for Chemical & Biological Sciences,
>> University of Karachi – 75270. Karachi-Pakistan.
>>
>> Contact No:
>> Office (92-21) 111222292 (Ext 309)
>> Email ID: saman.yousufali64.yahoo.com
>> saman.ali.iccs.edu
>>
>> |
>>
>>
>>
>> On Friday, February 12, 2016 1:00 AM, "amber-request.ambermd.org" <amber-request.ambermd.org> wrote:
>>
>>
>> Send AMBER mailing list submissions to
>> amber.ambermd.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://lists.ambermd.org/mailman/listinfo/amber
>> or, via email, send a message with subject or body 'help' to
>> amber-request.ambermd.org
>>
>> You can reach the person managing the list at
>> amber-owner.ambermd.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of AMBER digest..."
>>
>>
>> AMBER Mailing List Digest
>>
>> Today's Topics:
>>
>> 1. Re: citrulline parameters (Marie Brut)
>> 2. Re: MMPB (GB) SA cpptraj failed with prmtop (Arati Paudyal)
>> 3. Re: MMPB (GB) SA cpptraj failed with prmtop (Jason Swails)
>> 4. Gist Installation in Amber12 (Mongam Riba)
>> 5. minimization error : segmentation fault (Saman Yousuf ali)
>> 6. Re: minimization error : segmentation fault (Bill Ross)
>> 7. Is there a way to compare trajectories? (Karolina Markowska)
>> 8. Re: Is there a way to compare trajectories? (Bill Ross)
>> 9. Re: Is there a way to compare trajectories? (Dr. Anselm Horn)
>> 10. Re: Is there a way to compare trajectories? (Karolina Markowska)
>> 11. Restarting a heating simulation (Elisa Pieri)
>> 12. Re: Regarding MMGBSA calculation (neha chaudhary)
>> 13. Re: Is there a way to compare trajectories? (Carlos Simmerling)
>> 14. Re: Is there a way to compare trajectories? (Karolina Markowska)
>> 15. Re: Is there a way to compare trajectories?
>> (Mohammed Khaled Tumbi)
>> 16. Re: Gist Installation in Amber12 (David A Case)
>> 17. Amber 14 w/ CUDA - unclear "make test"-errors (Falko J?hnert)
>> 18. Re: Regarding MMGBSA calculation (David A Case)
>> 19. Re: MMPB (GB) SA cpptraj failed with prmtop (Arati Paudyal)
>> 20. Re: MMPB (GB) SA cpptraj failed with prmtop (Jason Swails)
>> 21. Re: Restarting a heating simulation (David A Case)
>> 22. Re: Restarting a heating simulation (Jason Swails)
>> 23. Re: Amber 14 w/ CUDA - unclear "make test"-errors (Jason Swails)
>> 24. Re: Restarting a heating simulation (Elisa Pieri)
>> 25. Re: Restarting a heating simulation (Carlos Simmerling)
>> 26. Re: Amber 14 w/ CUDA - unclear "make test"-errors (Falko J?hnert)
>> 27. Re: Is there a way to compare trajectories? (Daniel Roe)
>> 28. Re: Regarding MMGBSA calculation (Daniel Roe)
>> 29. Re: Amber 14 w/ CUDA - unclear "make test"-errors (Ross Walker)
>> 30. Re: Amber 14 w/ CUDA - unclear "make test"-errors (Ross Walker)
>> 31. Quasi-harmonic Calculations (Aronica, Pietro)
>> 32. Re: Is there a way to compare trajectories? (Osman, Roman)
>> 33. Re: Amber 14 w/ CUDA - unclear "make test"-errors (Jason Swails)
>> 34. Re: Quasi-harmonic Calculations (Jason Swails)
>> 35. Unable to run QM/MM with RNA and sodium ion (kaushik chakraborty)
>> 36. Re: Quasi-harmonic Calculations (Daniel Roe)
>> 37. interpret results (Carlos Romero)
>> 38. Error: Bad > topology file. (Batuhan Kav)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 10 Feb 2016 21:06:11 +0100
>> From: Marie Brut <marie.brut.laas.fr>
>> Subject: Re: [AMBER] citrulline parameters
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <3AFFF5EB-EF95-47A2-BBE0-683516D745DC.laas.fr>
>> Content-Type: text/plain; charset=utf-8
>>
>> Dear Karl,
>> Thank you so much for your detailed answer, it will help a lot.
>> I will try to follow the steps you describe?
>> All the best,
>> Marie
>>
>>
>> > Le 10 f?vr. 2016 ? 15:36, Karl Kirschner <k.n.kirschner.gmail.com> a ?crit :
>> >
>> > Hello Marie,
>> >
>> > Based on its structure, I would expect that the standard amino acids
>> > bonded and Lennard-Jones parameters (i.e. parm14SB) would be able to model
>> > a citrulline residue - or at least all terms should be present. What is
>> > left are the partial atomic charges, which need to be done using the resp
>> > protocol (ie. weighting factors of 0.0005 and 0.001) that was used for
>> > AMBER's amino acid residues. If no one has done this, then you will
>> > probably need to generate some conformations of a terminally capped
>> > citrulline in order to generate conformations for the resp calculations.
>> >
>> > Bests,
>> > Karl
>> >
>> > On Wed, Feb 10, 2016 at 3:13 PM, Marie Brut <marie.brut.laas.fr <mailto:marie.brut.laas.fr>> wrote:
>> >
>> >> Dear all,
>> >>
>> >> I need to introduce a citrulline residue in my protein and was wondering
>> >> if someone had already calculated citrulline parameters ?
>> >>
>> >> Many thanks for your help,
>> >>
>> >> Marie
>> >>
>> >>
>> >> Dr Marie Brut
>> >> Associate Professor - University of Toulouse
>> >> Atomic-scale Modeling of bio and bio-hybrid systems
>> >>
>> >> LAAS - CNRS
>> >> Nano Engineering and System Integration Team
>> >> 7 Avenue du Colonel Roche
>> >> BP 54200
>> >> 31031 Toulouse Cedex 4
>> >> Phone. : (+33) 5 61 33 63 04
>> >> Fax : (+33) 5 61 33 62 08
>> >> http://www.laas.fr/N2IS/ <http://www.laas.fr/N2IS/> <http://www.laas.fr/N2IS/ <http://www.laas.fr/N2IS/>>
>> >> https://homepages.laas.fr/mbrut/ <https://homepages.laas.fr/mbrut/> <https://homepages.laas.fr/mbrut/drupal/ <https://homepages.laas.fr/mbrut/drupal/>>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>> >> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>> > http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Wed, 10 Feb 2016 18:42:47 -0500
>> From: Arati Paudyal <apsilwal123.gmail.com>
>> Subject: Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAJomNAgX2Gt=39tLysq75NTZvutVSEHHkhAHgw5hgUhZROArmw.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Thanks Jason,
>>
>> Could you please provide some details on how one might access those hidden
>> files? Is it stores in some kind of files or do we need to extract it? I am
>> kind of new here in Amber. Any help would be greatly appreciated.
>>
>> Also, if I email you the original PDB and prmtop files, is there anyway you
>> would have time to look at those and see if I am doing anything wrong in
>> separating those two individual PDBs from the complex? I will email those
>> to your gmail if it is ok with you.
>>
>>
>>
>> Thanks again for your valuable time.
>>
>> On Wed, Feb 10, 2016 at 12:00 PM, Jason Swails <jason.swails.gmail.com>
>> wrote:
>>
>> > On Wed, Feb 10, 2016 at 10:53 AM, Arati Paudyal <apsilwal123.gmail.com>
>> > wrote:
>> >
>> > > Thanks for your reply,
>> > >
>> > > I will try to upgrade to Ambertools 15. But since the tutorial works just
>> > > fine, do you think this could be any issue related to upgrade though? I
>> > > will follow your suggestion and see how this goes.
>> > >
>> >
>> > ?We would need to see the output from cpptraj as it tried to compute
>> > surface areas. There's almost certainly an error message hidden in there
>> > that will tell us what the problem is.
>> >
>> > HTH,
>> > Jason
>> >
>> > --
>> > Jason M. Swails
>> > BioMaPS,
>> > Rutgers University
>> > Postdoctoral Researcher
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Wed, 10 Feb 2016 21:15:44 -0500
>> From: Jason Swails <jason.swails.gmail.com>
>> Subject: Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAEk9e3rryFHxn6BJ2d+SkS-6qJNFjFofU6YNMqqzK27GF3=VcA.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Have you tried yet with AmberTools 15?
>>
>> On Wed, Feb 10, 2016 at 6:42 PM, Arati Paudyal <apsilwal123.gmail.com>
>> wrote:
>>
>> > Thanks Jason,
>> >
>> > Could you please provide some details on how one might access those hidden
>> > files? Is it stores in some kind of files or do we need to extract it? I am
>> > kind of new here in Amber. Any help would be greatly appreciated.
>> >
>> > Also, if I email you the original PDB and prmtop files, is there anyway you
>> > would have time to look at those and see if I am doing anything wrong in
>> > separating those two individual PDBs from the complex? I will email those
>> > to your gmail if it is ok with you.
>> >
>> >
>> >
>> > Thanks again for your valuable time.
>> >
>> > On Wed, Feb 10, 2016 at 12:00 PM, Jason Swails <jason.swails.gmail.com>
>> > wrote:
>> >
>> > > On Wed, Feb 10, 2016 at 10:53 AM, Arati Paudyal <apsilwal123.gmail.com>
>> > > wrote:
>> > >
>> > > > Thanks for your reply,
>> > > >
>> > > > I will try to upgrade to Ambertools 15. But since the tutorial works
>> > just
>> > > > fine, do you think this could be any issue related to upgrade though? I
>> > > > will follow your suggestion and see how this goes.
>> > > >
>> > >
>> > > ?We would need to see the output from cpptraj as it tried to compute
>> > > surface areas. There's almost certainly an error message hidden in there
>> > > that will tell us what the problem is.
>> > >
>> > > HTH,
>> > > Jason
>> > >
>> > > --
>> > > Jason M. Swails
>> > > BioMaPS,
>> > > Rutgers University
>> > > Postdoctoral Researcher
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Thu, 11 Feb 2016 12:09:15 +0530
>> From: Mongam Riba <mongam12.gmail.com>
>> Subject: [AMBER] Gist Installation in Amber12
>> To: amber.ambermd.org
>> Message-ID:
>> <CAB=QPXt2sDvPwt+Rsjjng0EKsOKFa1v3QeHogHCYrB=WxpzHqA.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Hello,
>> i am a student perusing masters in bioinformatics. i am working on a
>> protein using amber 12 package and wanted to do the GIST analysis study.
>> but i am not able to run the gist analysis using cpptraj command. so is
>> there a way to install gist in amber12. if there then please can you help
>> me out i shall be very thankful to you.
>>
>>
>> with regards
>> Mongam Riba
>> Student of Bioscienc and bioinformatics
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Thu, 11 Feb 2016 07:34:09 +0000 (UTC)
>> From: Saman Yousuf ali <saman.yousufali64.yahoo.com>
>> Subject: [AMBER] minimization error : segmentation fault
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <1954759321.1976941.1455176049355.JavaMail.yahoo.mail.yahoo.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear all,I have tried to run minimization of apo protein. I have prepared topology files using ff14SB force field (amber14). Before running minimization, I checked my structure using cpptraj checkoverlap command to see if atoms are close to other atoms. I have found that protein contain some bad contact because leap added missing atoms then I started running minimization. I got the following error message. Sander runs for few cycles of minimization and stops with following error message (below)> minimization.inrestrain_min
>> ?&cntrl
>> ? imin?? = 1,
>> ? maxcyc = 500,
>> ? ntpr?? = 1,
>> ? ntb??? = 1,
>> ? cut??? = 10.0
>> ?/
>> Hold the system fixed
>> 25.0
>> RES 1 541
>> END
>> END
>> > sander -O -i min1.in -p protein.prmtop -c protein.inpcrd -o protein_min1.out -r protein_min1.rst -ref protein.inpcrd
>> > "ERROR MESSAGE"
>> Program received signal SIGSEGV: Segmentation fault - invalid memory reference.Backtrace for this error:
>> #0 0x33E3419497
>> #1 0x33E3419ADE
>> #2 0x36184358EF
>> #3 0x4D5DB5 in nb_adjust_
>> #4 0x4D7FE6 in ewald_force_
>> #5 0x64AFCF in force_
>> #6 0x484743 in runmin_
>> #7 0x47132F in sander_
>> #8 0x46CBBC in MAIN__ at multisander.F90:?
>> Segmentation fault (core dumped)
>> then I tried to minimize the same apo protein (with bad contact) via amber12 using ff99SB, minimization run perfectly with out any error message and I have completed all step then check structure again using cpptraj command. I found that after minimzation structure is fine (without any bad contacts). I used the following script for minimization,
>> >Minimization Amber12
>> ?&cntrl
>> ?imin=1, maxcyc=1000, ntmin = 2,
>> ?ntx = 1, ntc = 1, ntf = 1,
>> ?ntb = 1, ntp = 0, ncyc = 100,
>> ?ntwx = 1000, ntwe = 0, ntpr = 1000,
>> ?ntr = 1, cut = 10.0
>> ?&end
>> Restraints
>> ?25.0
>> RES 1 541
>> END
>> END
>> I want to know that why amber14 minimization failed while amber12 completed all minimization steps without any error message.
>> Thank you.
>>
>>
>> ?Best Regards,?Saman Yousuf AliJunior Research Fellow,
>> | Lab No. P-133, Computational Chemistry Laboratory
>> Dr. Panjwani Center for Molecular Medicine & Drug Research,
>> International Center for Chemical & Biological Sciences,
>> University of Karachi ? 75270.Karachi-Pakistan.
>>
>> Contact No:
>> Office (92-21) 111222292 (Ext 309)
>> Email ID:?saman.yousufali64.yahoo.com
>> saman.ali.iccs.edu
>>
>> ?? |
>>
>>
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Wed, 10 Feb 2016 23:39:50 -0800
>> From: Bill Ross <ross.cgl.ucsf.edu>
>> Subject: Re: [AMBER] minimization error : segmentation fault
>> To: amber.ambermd.org
>> Message-ID: <56BC3AC6.8050301.cgl.ucsf.edu>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>> Since you have ntpr=1, are any steps printed in the .out? If so, please
>> paste a few here.
>>
>> Bill
>>
>> On 2/10/16 11:34 PM, Saman Yousuf ali wrote:
>> > Dear all,I have tried to run minimization of apo protein. I have prepared topology files using ff14SB force field (amber14). Before running minimization, I checked my structure using cpptraj checkoverlap command to see if atoms are close to other atoms. I have found that protein contain some bad contact because leap added missing atoms then I started running minimization. I got the following error message. Sander runs for few cycles of minimization and stops with following error message (below)> minimization.inrestrain_min
>> > &cntrl
>> > imin = 1,
>> > maxcyc = 500,
>> > ntpr = 1,
>> > ntb = 1,
>> > cut = 10.0
>> > /
>> > Hold the system fixed
>> > 25.0
>> > RES 1 541
>> > END
>> > END
>> >> sander -O -i min1.in -p protein.prmtop -c protein.inpcrd -o protein_min1.out -r protein_min1.rst -ref protein.inpcrd
>> >> "ERROR MESSAGE"
>> > Program received signal SIGSEGV: Segmentation fault - invalid memory reference.Backtrace for this error:
>> > #0 0x33E3419497
>> > #1 0x33E3419ADE
>> > #2 0x36184358EF
>> > #3 0x4D5DB5 in nb_adjust_
>> > #4 0x4D7FE6 in ewald_force_
>> > #5 0x64AFCF in force_
>> > #6 0x484743 in runmin_
>> > #7 0x47132F in sander_
>> > #8 0x46CBBC in MAIN__ at multisander.F90:?
>> > Segmentation fault (core dumped)
>> > then I tried to minimize the same apo protein (with bad contact) via amber12 using ff99SB, minimization run perfectly with out any error message and I have completed all step then check structure again using cpptraj command. I found that after minimzation structure is fine (without any bad contacts). I used the following script for minimization,
>> >> Minimization Amber12
>> > &cntrl
>> > imin=1, maxcyc=1000, ntmin = 2,
>> > ntx = 1, ntc = 1, ntf = 1,
>> > ntb = 1, ntp = 0, ncyc = 100,
>> > ntwx = 1000, ntwe = 0, ntpr = 1000,
>> > ntr = 1, cut = 10.0
>> > &end
>> > Restraints
>> > 25.0
>> > RES 1 541
>> > END
>> > END
>> > I want to know that why amber14 minimization failed while amber12 completed all minimization steps without any error message.
>> > Thank you.
>> >
>> >
>> > Best Regards, Saman Yousuf AliJunior Research Fellow,
>> > | Lab No. P-133, Computational Chemistry Laboratory
>> > Dr. Panjwani Center for Molecular Medicine & Drug Research,
>> > International Center for Chemical & Biological Sciences,
>> > University of Karachi ? 75270.Karachi-Pakistan.
>> >
>> > Contact No:
>> > Office (92-21) 111222292 (Ext 309)
>> > Email ID: saman.yousufali64.yahoo.com
>> > saman.ali.iccs.edu
>> >
>> > |
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 7
>> Date: Thu, 11 Feb 2016 10:07:01 +0100
>> From: Karolina Markowska <markowska.kar.gmail.com>
>> Subject: [AMBER] Is there a way to compare trajectories?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAFtT2ZxGXxaz8dqA-FPhz=GRcALv=ExmpyvF-U4por+9Lkjejg.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear Amber Users,
>>
>> I have two simulations with the same system and I would like to compare
>> them. Mostly I would like to check if I'm having the same protein
>> conformations in these two simulations. Does Amber software provide a tool
>> for that kind of analysis?
>>
>> I wanted to use cpptraj and use the first trajectory as reference, add the
>> second one by trajin and calculate rmsd between them, but cpptraj uses only
>> the first frame from that file. Can I make cpptraj to read whole trajectory
>> as a reference?
>> The script looked like that:
>>
>> parm protein.prmtop
>> reference sim1.nc
>> trajin sim2.nc
>> autoimage
>> strip :WAT
>> strip :Na+
>> rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass
>> quit
>>
>> | sim1.nc is the trajectory of the first simulation and sim2.nc is the
>> trajectory from the second simulation.
>>
>> Thanks for your help.
>> Best regards,
>> Karolina Markowska
>> PhD student
>>
>>
>> ------------------------------
>>
>> Message: 8
>> Date: Thu, 11 Feb 2016 01:19:49 -0800
>> From: Bill Ross <ross.cgl.ucsf.edu>
>> Subject: Re: [AMBER] Is there a way to compare trajectories?
>> To: amber.ambermd.org
>> Message-ID: <56BC5235.70005.cgl.ucsf.edu>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>> A frame-by-frame comparison of two trajectories might have value for
>> debugging code, but I'm not sure what the meaning would be otherwise. I
>> speak from having actually implemented this feature in an old program.
>>
>> I think you might do better if you can derive clusters of conformations
>> from each trajectory and comparing those, or just compare minimized
>> averages of the trajectories if the conformations don't change much.
>>
>> Bill
>>
>> On 2/11/16 1:07 AM, Karolina Markowska wrote:
>> > Dear Amber Users,
>> >
>> > I have two simulations with the same system and I would like to compare
>> > them. Mostly I would like to check if I'm having the same protein
>> > conformations in these two simulations. Does Amber software provide a tool
>> > for that kind of analysis?
>> >
>> > I wanted to use cpptraj and use the first trajectory as reference, add the
>> > second one by trajin and calculate rmsd between them, but cpptraj uses only
>> > the first frame from that file. Can I make cpptraj to read whole trajectory
>> > as a reference?
>> > The script looked like that:
>> >
>> > parm protein.prmtop
>> > reference sim1.nc
>> > trajin sim2.nc
>> > autoimage
>> > strip :WAT
>> > strip :Na+
>> > rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass
>> > quit
>> >
>> > | sim1.nc is the trajectory of the first simulation and sim2.nc is the
>> > trajectory from the second simulation.
>> >
>> > Thanks for your help.
>> > Best regards,
>> > Karolina Markowska
>> > PhD student
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 9
>> Date: Thu, 11 Feb 2016 10:27:03 +0100
>> From: "Dr. Anselm Horn" <anselm.horn.fau.de>
>> Subject: Re: [AMBER] Is there a way to compare trajectories?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <56BC53E7.5070100.fau.de>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Dear Karolina,
>>
>> AFAIK a 'reference' is limited to a single structure.
>>
>> Reading in two trajectories in a row should be no problem for cpptraj,
>> as you can give several trajin commands.
>> For the comparison of the two trajectories you could then use e.g. a
>> 2D-RMSD-plot or perform a cluster analysis on the combined trajectories
>> with a subsequent inspection of the distribution of the cluster
>> structures between the trajectories. Or you could monitor some other
>> properties of interest and compare those values.
>>
>> Regards,
>>
>> Anselm
>>
>>
>> Am 11.02.2016 10:07, schrieb Karolina Markowska:
>> > Dear Amber Users,
>> >
>> > I have two simulations with the same system and I would like to compare
>> > them. Mostly I would like to check if I'm having the same protein
>> > conformations in these two simulations. Does Amber software provide a tool
>> > for that kind of analysis?
>> >
>> > I wanted to use cpptraj and use the first trajectory as reference, add the
>> > second one by trajin and calculate rmsd between them, but cpptraj uses only
>> > the first frame from that file. Can I make cpptraj to read whole trajectory
>> > as a reference?
>> > The script looked like that:
>> >
>> > parm protein.prmtop
>> > reference sim1.nc
>> > trajin sim2.nc
>> > autoimage
>> > strip :WAT
>> > strip :Na+
>> > rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass
>> > quit
>> >
>> > | sim1.nc is the trajectory of the first simulation and sim2.nc is the
>> > trajectory from the second simulation.
>> >
>> > Thanks for your help.
>> > Best regards,
>> > Karolina Markowska
>> > PhD student
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 10
>> Date: Thu, 11 Feb 2016 10:44:52 +0100
>> From: Karolina Markowska <markowska.kar.gmail.com>
>> Subject: Re: [AMBER] Is there a way to compare trajectories?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAFtT2ZzS0kqwz3DEBwbbbo5vwP5mLEzANK1C_h=BTUSdwkrboA.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Thank you, Bill and Anselm for your advices,
>>
>> I think I will try the 2D-RMSD-plot first.
>>
>> Have a nice day!
>> Karolina
>>
>> 2016-02-11 10:27 GMT+01:00 Dr. Anselm Horn <anselm.horn.fau.de>:
>>
>> > Dear Karolina,
>> >
>> > AFAIK a 'reference' is limited to a single structure.
>> >
>> > Reading in two trajectories in a row should be no problem for cpptraj,
>> > as you can give several trajin commands.
>> > For the comparison of the two trajectories you could then use e.g. a
>> > 2D-RMSD-plot or perform a cluster analysis on the combined trajectories
>> > with a subsequent inspection of the distribution of the cluster
>> > structures between the trajectories. Or you could monitor some other
>> > properties of interest and compare those values.
>> >
>> > Regards,
>> >
>> > Anselm
>> >
>> >
>> > Am 11.02.2016 10:07, schrieb Karolina Markowska:
>> > > Dear Amber Users,
>> > >
>> > > I have two simulations with the same system and I would like to compare
>> > > them. Mostly I would like to check if I'm having the same protein
>> > > conformations in these two simulations. Does Amber software provide a
>> > tool
>> > > for that kind of analysis?
>> > >
>> > > I wanted to use cpptraj and use the first trajectory as reference, add
>> > the
>> > > second one by trajin and calculate rmsd between them, but cpptraj uses
>> > only
>> > > the first frame from that file. Can I make cpptraj to read whole
>> > trajectory
>> > > as a reference?
>> > > The script looked like that:
>> > >
>> > > parm protein.prmtop
>> > > reference sim1.nc
>> > > trajin sim2.nc
>> > > autoimage
>> > > strip :WAT
>> > > strip :Na+
>> > > rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass
>> > > quit
>> > >
>> > > | sim1.nc is the trajectory of the first simulation and sim2.nc is the
>> > > trajectory from the second simulation.
>> > >
>> > > Thanks for your help.
>> > > Best regards,
>> > > Karolina Markowska
>> > > PhD student
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > >
>> >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> ------------------------------
>>
>> Message: 11
>> Date: Thu, 11 Feb 2016 11:43:50 +0100
>> From: Elisa Pieri <elisa.pieri90.gmail.com>
>> Subject: [AMBER] Restarting a heating simulation
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CANYcjuZH3R0gXHxiJ9TTnXzvJTF2pS=rv3co9Kuvi7AjwSEAdg.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear all,
>>
>> I'm heating my system, but the maximum walltime in my cluster is 1 week,
>> that won't probably be enough. This in my current input:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *Implicit solvent constant pH initial heating mdin &cntrl imin=0,
>> irest=0, ntx=1, ntpr=500, ntwx=500, nstlim=1000000, dt=0.002, ntt=3,
>> tempi=10, temp0=300, tautp=2.0, ig=-1, ntp=0, ntc=2, ntf=2,
>> cut=30, ntb=0, igb=2, tol=0.000001, nrespa=1, saltcon=0.1,
>> icnstph=1, ntcnstph=100000000, gamma_ln=5.0, ntwr=500, ioutfm=1,
>> nmropt=1, / &wt TYPE='TEMP0', ISTEP1=1, ISTEP2=500000, VALUE1=10.0,
>> VALUE2=300.0, / &wt TYPE='END' /*
>>
>> First of all..my system has 3744 atoms and I'm running pmemd on 36 cores
>> (Intel X5675 3.06 GHz). It has an average of 10.5 minutes per picosecond,
>> so it will take more than two weeks to finish. Is it normal? Isn't it VERY
>> slow?
>>
>> Second, what do I have to change in the input file when I'll have to
>> restart the simulation?
>>
>> Thanks,
>> Elisa
>>
>>
>> ------------------------------
>>
>> Message: 12
>> Date: Thu, 11 Feb 2016 16:15:44 +0530
>> From: neha chaudhary <nehachaudhary769.gmail.com>
>> Subject: Re: [AMBER] Regarding MMGBSA calculation
>> To: david.case.rutgers.edu, AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CANRroAEFZc7m2AaV0emOwjP-9vP82NH+pr2xYUykhSkSjZup6A.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Hello Sir,
>>
>> I tried the command in server as /share/apps/amber/amber12/bin/cpptraj, Fatal
>> Error: This program was not built to run in your system.
>> Someone else installed the program on the server.
>>
>> Best Regards,
>>
>> *Neha*
>>
>> Research Scholar,
>> Centre for Computational Biology and Bioinformatics,
>> School of Life Sciences,
>> Central University of Himachal Pradesh,
>>
>>
>>
>>
>>
>> On Sat, Feb 6, 2016 at 6:54 PM, David A Case <david.case.rutgers.edu> wrote:
>>
>> > On Sat, Feb 06, 2016, neha chaudhary wrote:
>> > >
>> > > I am using amber on a server, when I am runnung
>> > /share/apps/amber/amber12/
>> > > bin/cpptraj, Fatal Error: This program was not built to run in your
>> > system.
>> > > Please verify that both the operating system and the processor support
>> > > Intel(R) AVX.
>> >
>> > Did you try any of the advice that Jason or I gave to your last email? (My
>> > response is given below.) Did you install Amber yourself, or did someone
>> > else
>> > do it?
>> >
>> > ...dac
>> >
>> > > >
>> > > > What happens if you type "/share/apps/amber/amber12/bin/cpptraj" at a
>> > > > console prompt? Do the Amber test cases mostly pass?
>> > > >
>> > > > Related question, especially if you get failures from the previous
>> > > > questions:
>> > > > what OS and compiler are you using? what arguments did you give to
>> > Amber's
>> > > > configure script?
>> > > >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> ------------------------------
>>
>> Message: 13
>> Date: Thu, 11 Feb 2016 06:15:39 -0500
>> From: Carlos Simmerling <carlos.simmerling.gmail.com>
>> Subject: Re: [AMBER] Is there a way to compare trajectories?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAGk3s-RNboftknaV4r0t87jLW0V6sRur+CYvEJ2GY2swXN-v2g.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> We frequently read in 2 trajectories then do cluster analysis, and compare
>> the population of each cluster in trajectory 1 vs 2.this gives you error
>> bars on the population of each cluster. It's similar to 2drmsd but gives
>> you something more quantitative.
>> On Feb 11, 2016 4:27 AM, "Dr. Anselm Horn" <anselm.horn.fau.de> wrote:
>>
>> > Dear Karolina,
>> >
>> > AFAIK a 'reference' is limited to a single structure.
>> >
>> > Reading in two trajectories in a row should be no problem for cpptraj,
>> > as you can give several trajin commands.
>> > For the comparison of the two trajectories you could then use e.g. a
>> > 2D-RMSD-plot or perform a cluster analysis on the combined trajectories
>> > with a subsequent inspection of the distribution of the cluster
>> > structures between the trajectories. Or you could monitor some other
>> > properties of interest and compare those values.
>> >
>> > Regards,
>> >
>> > Anselm
>> >
>> >
>> > Am 11.02.2016 10:07, schrieb Karolina Markowska:
>> > > Dear Amber Users,
>> > >
>> > > I have two simulations with the same system and I would like to compare
>> > > them. Mostly I would like to check if I'm having the same protein
>> > > conformations in these two simulations. Does Amber software provide a
>> > tool
>> > > for that kind of analysis?
>> > >
>> > > I wanted to use cpptraj and use the first trajectory as reference, add
>> > the
>> > > second one by trajin and calculate rmsd between them, but cpptraj uses
>> > only
>> > > the first frame from that file. Can I make cpptraj to read whole
>> > trajectory
>> > > as a reference?
>> > > The script looked like that:
>> > >
>> > > parm protein.prmtop
>> > > reference sim1.nc
>> > > trajin sim2.nc
>> > > autoimage
>> > > strip :WAT
>> > > strip :Na+
>> > > rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass
>> > > quit
>> > >
>> > > | sim1.nc is the trajectory of the first simulation and sim2.nc is the
>> > > trajectory from the second simulation.
>> > >
>> > > Thanks for your help.
>> > > Best regards,
>> > > Karolina Markowska
>> > > PhD student
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > >
>> >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> ------------------------------
>>
>> Message: 14
>> Date: Thu, 11 Feb 2016 12:27:46 +0100
>> From: Karolina Markowska <markowska.kar.gmail.com>
>> Subject: Re: [AMBER] Is there a way to compare trajectories?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAFtT2ZyLiRKmKgXdGcd3+WZ15vGZ7O+eHD0B9U7tDs9r0pB25w.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Thank you, Carlos, that's even better!
>>
>> Karolina
>>
>> 2016-02-11 12:15 GMT+01:00 Carlos Simmerling <carlos.simmerling.gmail.com>:
>>
>> > We frequently read in 2 trajectories then do cluster analysis, and compare
>> > the population of each cluster in trajectory 1 vs 2.this gives you error
>> > bars on the population of each cluster. It's similar to 2drmsd but gives
>> > you something more quantitative.
>> > On Feb 11, 2016 4:27 AM, "Dr. Anselm Horn" <anselm.horn.fau.de> wrote:
>> >
>> > > Dear Karolina,
>> > >
>> > > AFAIK a 'reference' is limited to a single structure.
>> > >
>> > > Reading in two trajectories in a row should be no problem for cpptraj,
>> > > as you can give several trajin commands.
>> > > For the comparison of the two trajectories you could then use e.g. a
>> > > 2D-RMSD-plot or perform a cluster analysis on the combined trajectories
>> > > with a subsequent inspection of the distribution of the cluster
>> > > structures between the trajectories. Or you could monitor some other
>> > > properties of interest and compare those values.
>> > >
>> > > Regards,
>> > >
>> > > Anselm
>> > >
>> > >
>> > > Am 11.02.2016 10:07, schrieb Karolina Markowska:
>> > > > Dear Amber Users,
>> > > >
>> > > > I have two simulations with the same system and I would like to compare
>> > > > them. Mostly I would like to check if I'm having the same protein
>> > > > conformations in these two simulations. Does Amber software provide a
>> > > tool
>> > > > for that kind of analysis?
>> > > >
>> > > > I wanted to use cpptraj and use the first trajectory as reference, add
>> > > the
>> > > > second one by trajin and calculate rmsd between them, but cpptraj uses
>> > > only
>> > > > the first frame from that file. Can I make cpptraj to read whole
>> > > trajectory
>> > > > as a reference?
>> > > > The script looked like that:
>> > > >
>> > > > parm protein.prmtop
>> > > > reference sim1.nc
>> > > > trajin sim2.nc
>> > > > autoimage
>> > > > strip :WAT
>> > > > strip :Na+
>> > > > rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass
>> > > > quit
>> > > >
>> > > > | sim1.nc is the trajectory of the first simulation and sim2.nc is the
>> > > > trajectory from the second simulation.
>> > > >
>> > > > Thanks for your help.
>> > > > Best regards,
>> > > > Karolina Markowska
>> > > > PhD student
>> > > > _______________________________________________
>> > > > AMBER mailing list
>> > > > AMBER.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > >
>> > > >
>> > >
>> > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> ------------------------------
>>
>> Message: 15
>> Date: Thu, 11 Feb 2016 11:30:50 +0000
>> From: Mohammed Khaled Tumbi <khaledtumbi.gmail.com>
>> Subject: Re: [AMBER] Is there a way to compare trajectories?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAEJ44H=b37P+AyM0s34C4HOTwnqhYsVGCzQHGga-9Cs7VPmyKA.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear Markowska:
>> For comparison of you can use pyPcazip.
>> "" Trajectory compression with *pyPcazip* provides the gateway to a range
>> of analysis methods that provide objective, quantitative and comparative
>> metrics related to convergence and sampling, and the *similarity between
>> one trajectory and another. "". *
>>
>> https://bitbucket.org/ramonbsc/pypcazip/overview
>> https://pypi.python.org/pypi/pyPcazip
>> This program can compare trajectories based on RMSD, PCA analysis.
>>
>>
>> On Thu, 11 Feb 2016 at 11:16 Carlos Simmerling <carlos.simmerling.gmail.com>
>> wrote:
>>
>> > We frequently read in 2 trajectories then do cluster analysis, and compare
>> > the population of each cluster in trajectory 1 vs 2.this gives you error
>> > bars on the population of each cluster. It's similar to 2drmsd but gives
>> > you something more quantitative.
>> > On Feb 11, 2016 4:27 AM, "Dr. Anselm Horn" <anselm.horn.fau.de> wrote:
>> >
>> > > Dear Karolina,
>> > >
>> > > AFAIK a 'reference' is limited to a single structure.
>> > >
>> > > Reading in two trajectories in a row should be no problem for cpptraj,
>> > > as you can give several trajin commands.
>> > > For the comparison of the two trajectories you could then use e.g. a
>> > > 2D-RMSD-plot or perform a cluster analysis on the combined trajectories
>> > > with a subsequent inspection of the distribution of the cluster
>> > > structures between the trajectories. Or you could monitor some other
>> > > properties of interest and compare those values.
>> > >
>> > > Regards,
>> > >
>> > > Anselm
>> > >
>> > >
>> > > Am 11.02.2016 10:07, schrieb Karolina Markowska:
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> --
>> --------------------------------------------------------
>> Tumbi Mohammed Khaled.
>>
>>
>> ------------------------------
>>
>> Message: 16
>> Date: Thu, 11 Feb 2016 21:17:03 +0900
>> From: David A Case <david.case.rutgers.edu>
>> Subject: Re: [AMBER] Gist Installation in Amber12
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <20160211121703.GA9977.scarletmail.rutgers.edu>
>> Content-Type: text/plain; charset=us-ascii
>>
>> On Thu, Feb 11, 2016, Mongam Riba wrote:
>>
>> > i am a student perusing masters in bioinformatics. i am working on a
>> > protein using amber 12 package and wanted to do the GIST analysis study.
>> > but i am not able to run the gist analysis using cpptraj command. so is
>> > there a way to install gist in amber12. if there then please can you help
>> > me out i shall be very thankful to you.
>>
>> The gist analysis is a part of cpptraj in AmberTools, which is freely
>> available. You should download and install AmberTools15 (in a separate
>> directory tree: the top of the Amber12 tree is .../amber12, whereas the top of
>> the AmberTools15 tree will be .../amber14.) You can use the trajectories that
>> you generate with Amber12 as input to the gist analysis in AmberTools15.
>>
>> ...good luck....dac
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 17
>> Date: Thu, 11 Feb 2016 13:36:50 +0100
>> From: Falko J?hnert <falko.jaehnert.biochemtech.uni-halle.de>
>> Subject: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors
>> To: amber.ambermd.org
>> Message-ID: <000201d164c8$e4005980$ac010c80$.biochemtech.uni-halle.de>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Dear Amberlings,
>>
>>
>>
>> at first, thanks a lot helping me out with my last problem ?Howto cpptraj -
>> multiple trajin-commands in one line?. .Jean-Marc Billod: I did it your way
>> and this works just fine!
>>
>>
>>
>> Now I?ve got a little concern about the results of my installation of Amber
>> 14. The make test-procedure at the parallel installation level (both with 2
>> and 4 threads) went through without a single error, even without rounding
>> mistakes. After that i?ve compiled Amber 14 the usual way to gather
>> CUDA-support. Now the make test produce some rounding errors which are okay
>> (I hope), but also errors where lines one of the compared files (*.diff) are
>> inserted and thus produce a lot of differences. If one compares the numbers
>> of the correctly aligned lines then everything is fine (I hope ? again with
>> some rounding errors). To understand my problem better I attached the *log-
>> and the *.diff-files which are shortened to display only the unclear diffs.
>>
>>
>>
>> Can I ignore this diffs safely? If not, may someone provide any information
>> handling this problem?
>>
>>
>>
>> Thanks a lot in advance! Kind regards,
>>
>> Falko Jaehnert.
>>
>>
>>
>>
>>
>> -------------- next part --------------
>> A non-text attachment was scrubbed...
>> Name: 2016-02-09_09-33-40_short.diff
>> Type: application/octet-stream
>> Size: 64750 bytes
>> Desc: not available
>> Url : http://lists.ambermd.org/mailman/private/amber/attachments/20160211/d5fa555a/attachment-0002.obj
>> -------------- next part --------------
>> A non-text attachment was scrubbed...
>> Name: 2016-02-09_09-33-40_short.log
>> Type: application/octet-stream
>> Size: 1880 bytes
>> Desc: not available
>> Url : http://lists.ambermd.org/mailman/private/amber/attachments/20160211/d5fa555a/attachment-0003.obj
>>
>> ------------------------------
>>
>> Message: 18
>> Date: Thu, 11 Feb 2016 21:45:22 +0900
>> From: David A Case <david.case.rutgers.edu>
>> Subject: Re: [AMBER] Regarding MMGBSA calculation
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <20160211124522.GB9977.scarletmail.rutgers.edu>
>> Content-Type: text/plain; charset=us-ascii
>>
>> On Thu, Feb 11, 2016, neha chaudhary wrote:
>> >
>> > I tried the command in server as /share/apps/amber/amber12/bin/cpptraj, Fatal
>> > Error: This program was not built to run in your system.
>>
>> > Someone else installed the program on the server.
>>
>> There is no way that anyone on the list will be able to help. You should
>> consider just installing AmberTools yourself (it is quite easy, assuming that
>> the node on which you are compiling things is the same as the nodes on which
>> it will be run).
>>
>> Otherwise, you will need to contact the person who installed the program and
>> report the problem to that person.
>>
>> ....dac
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 19
>> Date: Thu, 11 Feb 2016 07:47:00 -0500
>> From: Arati Paudyal <apsilwal123.gmail.com>
>> Subject: Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAJomNAhdXtrNdd07qgL6igJjvCRX6gEaxeE-CD4HRd=EFiHSvg.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Jason,
>>
>> I tried a short run with AmberTools 15 and I still get the same error
>> message. I re-ran the tutorial and it runs fine with AmberTools 15 as well.
>>
>> On Wed, Feb 10, 2016 at 9:15 PM, Jason Swails <jason.swails.gmail.com>
>> wrote:
>>
>> > Have you tried yet with AmberTools 15?
>> >
>> > On Wed, Feb 10, 2016 at 6:42 PM, Arati Paudyal <apsilwal123.gmail.com>
>> > wrote:
>> >
>> > > Thanks Jason,
>> > >
>> > > Could you please provide some details on how one might access those
>> > hidden
>> > > files? Is it stores in some kind of files or do we need to extract it? I
>> > am
>> > > kind of new here in Amber. Any help would be greatly appreciated.
>> > >
>> > > Also, if I email you the original PDB and prmtop files, is there anyway
>> > you
>> > > would have time to look at those and see if I am doing anything wrong in
>> > > separating those two individual PDBs from the complex? I will email those
>> > > to your gmail if it is ok with you.
>> > >
>> > >
>> > >
>> > > Thanks again for your valuable time.
>> > >
>> > > On Wed, Feb 10, 2016 at 12:00 PM, Jason Swails <jason.swails.gmail.com>
>> > > wrote:
>> > >
>> > > > On Wed, Feb 10, 2016 at 10:53 AM, Arati Paudyal <apsilwal123.gmail.com
>> > >
>> > > > wrote:
>> > > >
>> > > > > Thanks for your reply,
>> > > > >
>> > > > > I will try to upgrade to Ambertools 15. But since the tutorial works
>> > > just
>> > > > > fine, do you think this could be any issue related to upgrade
>> > though? I
>> > > > > will follow your suggestion and see how this goes.
>> > > > >
>> > > >
>> > > > ?We would need to see the output from cpptraj as it tried to compute
>> > > > surface areas. There's almost certainly an error message hidden in
>> > there
>> > > > that will tell us what the problem is.
>> > > >
>> > > > HTH,
>> > > > Jason
>> > > >
>> > > > --
>> > > > Jason M. Swails
>> > > > BioMaPS,
>> > > > Rutgers University
>> > > > Postdoctoral Researcher
>> > > > _______________________________________________
>> > > > AMBER mailing list
>> > > > AMBER.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> >
>> >
>> >
>> > --
>> > Jason M. Swails
>> > BioMaPS,
>> > Rutgers University
>> > Postdoctoral Researcher
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> ------------------------------
>>
>> Message: 20
>> Date: Thu, 11 Feb 2016 07:50:09 -0500
>> From: Jason Swails <jason.swails.gmail.com>
>> Subject: Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAEk9e3phs6JrA_H-E1F7+yXsGSPBHV1LoK14PqKNgC4z4pPt0g.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Can you send me the prmtop files, input file, and a trajectory with ~2 to 3
>> frames so I can try to reproduce this?
>>
>> On Thu, Feb 11, 2016 at 7:47 AM, Arati Paudyal <apsilwal123.gmail.com>
>> wrote:
>>
>> > Jason,
>> >
>> > I tried a short run with AmberTools 15 and I still get the same error
>> > message. I re-ran the tutorial and it runs fine with AmberTools 15 as well.
>> >
>> > On Wed, Feb 10, 2016 at 9:15 PM, Jason Swails <jason.swails.gmail.com>
>> > wrote:
>> >
>> > > Have you tried yet with AmberTools 15?
>> > >
>> > > On Wed, Feb 10, 2016 at 6:42 PM, Arati Paudyal <apsilwal123.gmail.com>
>> > > wrote:
>> > >
>> > > > Thanks Jason,
>> > > >
>> > > > Could you please provide some details on how one might access those
>> > > hidden
>> > > > files? Is it stores in some kind of files or do we need to extract it?
>> > I
>> > > am
>> > > > kind of new here in Amber. Any help would be greatly appreciated.
>> > > >
>> > > > Also, if I email you the original PDB and prmtop files, is there anyway
>> > > you
>> > > > would have time to look at those and see if I am doing anything wrong
>> > in
>> > > > separating those two individual PDBs from the complex? I will email
>> > those
>> > > > to your gmail if it is ok with you.
>> > > >
>> > > >
>> > > >
>> > > > Thanks again for your valuable time.
>> > > >
>> > > > On Wed, Feb 10, 2016 at 12:00 PM, Jason Swails <jason.swails.gmail.com
>> > >
>> > > > wrote:
>> > > >
>> > > > > On Wed, Feb 10, 2016 at 10:53 AM, Arati Paudyal <
>> > apsilwal123.gmail.com
>> > > >
>> > > > > wrote:
>> > > > >
>> > > > > > Thanks for your reply,
>> > > > > >
>> > > > > > I will try to upgrade to Ambertools 15. But since the tutorial
>> > works
>> > > > just
>> > > > > > fine, do you think this could be any issue related to upgrade
>> > > though? I
>> > > > > > will follow your suggestion and see how this goes.
>> > > > > >
>> > > > >
>> > > > > ?We would need to see the output from cpptraj as it tried to compute
>> > > > > surface areas. There's almost certainly an error message hidden in
>> > > there
>> > > > > that will tell us what the problem is.
>> > > > >
>> > > > > HTH,
>> > > > > Jason
>> > > > >
>> > > > > --
>> > > > > Jason M. Swails
>> > > > > BioMaPS,
>> > > > > Rutgers University
>> > > > > Postdoctoral Researcher
>> > > > > _______________________________________________
>> > > > > AMBER mailing list
>> > > > > AMBER.ambermd.org
>> > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > >
>> > > > _______________________________________________
>> > > > AMBER mailing list
>> > > > AMBER.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > Jason M. Swails
>> > > BioMaPS,
>> > > Rutgers University
>> > > Postdoctoral Researcher
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> ------------------------------
>>
>> Message: 21
>> Date: Thu, 11 Feb 2016 21:50:39 +0900
>> From: David A Case <david.case.rutgers.edu>
>> Subject: Re: [AMBER] Restarting a heating simulation
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <20160211125039.GC9977.scarletmail.rutgers.edu>
>> Content-Type: text/plain; charset=us-ascii
>>
>> On Thu, Feb 11, 2016, Elisa Pieri wrote:
>> >
>> > *Implicit solvent constant pH initial heating mdin &cntrl imin=0,
>> > irest=0, ntx=1, ntpr=500, ntwx=500, nstlim=1000000, dt=0.002, ntt=3,
>> > tempi=10, temp0=300, tautp=2.0, ig=-1, ntp=0, ntc=2, ntf=2,
>> > cut=30, ntb=0, igb=2, tol=0.000001, nrespa=1, saltcon=0.1,
>> > icnstph=1, ntcnstph=100000000, gamma_ln=5.0, ntwr=500, ioutfm=1,
>> > nmropt=1, / &wt TYPE='TEMP0', ISTEP1=1, ISTEP2=500000, VALUE1=10.0,
>> > VALUE2=300.0, / &wt TYPE='END' /*
>> >
>> > First of all..my system has 3744 atoms and I'm running pmemd on 36 cores
>> > (Intel X5675 3.06 GHz). It has an average of 10.5 minutes per picosecond,
>> > so it will take more than two weeks to finish. Is it normal? Isn't it VERY
>> > slow?
>>
>> Try reducing the cutoff (to say, 20 Ang.). Also see if lowering the number of
>> cores makes the program go faster (depends a *lot* on the details of your
>> machine, so it is hard to make generalizations.) Also check whether the
>> presence of a non-zero value for icnstph is having an effect on timings.
>>
>> If you do the run in pieces, set ntx=5 and irest=1 when you restart, using
>> the restart file from the first run as the input to the second run.
>>
>> ....dac
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 22
>> Date: Thu, 11 Feb 2016 08:00:24 -0500
>> From: Jason Swails <jason.swails.gmail.com>
>> Subject: Re: [AMBER] Restarting a heating simulation
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAEk9e3qzee05O3DY-oH56Qd8UzgAwPq39NuGxUYti-N8KENXvg.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> On Thu, Feb 11, 2016 at 5:43 AM, Elisa Pieri <elisa.pieri90.gmail.com>
>> wrote:
>>
>> > Dear all,
>> >
>> > I'm heating my system, but the maximum walltime in my cluster is 1 week,
>> > that won't probably be enough. This in my current input:
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > *Implicit solvent constant pH initial heating mdin &cntrl imin=0,
>> > irest=0, ntx=1, ntpr=500, ntwx=500, nstlim=1000000, dt=0.002, ntt=3,
>> > tempi=10, temp0=300, tautp=2.0, ig=-1, ntp=0, ntc=2, ntf=2,
>> > cut=30, ntb=0, igb=2, tol=0.000001, nrespa=1, saltcon=0.1,
>> > icnstph=1, ntcnstph=100000000, gamma_ln=5.0, ntwr=500, ioutfm=1,
>> > nmropt=1, / &wt TYPE='TEMP0', ISTEP1=1, ISTEP2=500000, VALUE1=10.0,
>> > VALUE2=300.0, / &wt TYPE='END' /*
>> >
>> > First of all..my system has 3744 atoms and I'm running pmemd on 36 cores
>> > (Intel X5675 3.06 GHz). It has an average of 10.5 minutes per picosecond,
>> > so it will take more than two weeks to finish. Is it normal? Isn't it VERY
>> > slow?
>> >
>>
>> ?How exactly are you running in parallel? (i.e., what is the exact command
>> that you are using?) There are a number of possible issues.
>>
>> A common mistake people make trying to run pmemd in parallel is to use a
>> command that looks like
>>
>> mpirun -np 36 pmemd -O -i mdin ...
>>
>> The problem here is that pmemd (and sander) are serial executables that are
>> incapable of parallelizing their calculation. The correct thing to do is
>>
>> mpirun -np 36 pmemd.MPI -O -i ...
>>
>> If you use pmemd instead of pmemd.MPI, then you will get the exact same
>> performance as running on 1 CPU (perhaps worse if the CPUs are
>> oversubscribed). It's also possible if you are asking for multiple nodes
>> that all of the threads are running on a single node (which will slow down
>> performance substantially). You'd have to ask your help staff to figure
>> out if that's happening (and how to fix it), though.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> ------------------------------
>>
>> Message: 23
>> Date: Thu, 11 Feb 2016 08:03:19 -0500
>> From: Jason Swails <jason.swails.gmail.com>
>> Subject: Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAEk9e3pWj7TeemNVMkZvrwi2xSLSqTgnJXS2L2js9gtoh938cg.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> On Thu, Feb 11, 2016 at 7:36 AM, Falko J?hnert <
>> falko.jaehnert.biochemtech.uni-halle.de> wrote:
>>
>> > Dear Amberlings,
>> >
>> >
>> >
>> > at first, thanks a lot helping me out with my last problem ?Howto cpptraj -
>> > multiple trajin-commands in one line?. @Jean-Marc Billod: I did it your way
>> > and this works just fine!
>> >
>> >
>> >
>> > Now I?ve got a little concern about the results of my installation of Amber
>> > 14. The make test-procedure at the parallel installation level (both with 2
>> > and 4 threads) went through without a single error, even without rounding
>> > mistakes. After that i?ve compiled Amber 14 the usual way to gather
>> > CUDA-support. Now the make test produce some rounding errors which are okay
>> > (I hope), but also errors where lines one of the compared files (*.diff)
>> > are
>> > inserted and thus produce a lot of differences. If one compares the numbers
>> > of the correctly aligned lines then everything is fine (I hope ? again with
>> > some rounding errors). To understand my problem better I attached the *log-
>> > and the *.diff-files which are shortened to display only the unclear diffs.
>> >
>> >
>> >
>> > Can I ignore this diffs safely? If not, may someone provide any information
>> > handling this problem?
>> >
>>
>> ?This is a known deficiency in the CUDA testing infrastructure. All of the
>> larger failures (i.e., that are not round-off) arise from stochastic
>> methods (ntt=2 or ntt=3) where the random number stream is different on
>> every GPU.
>>
>> While there is a way to fix it (and it is on the to-do list), it apparently
>> hasn't been important enough to make it to the top yet.
>>
>> HTH,
>> Jason
>> ?
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> ------------------------------
>>
>> Message: 24
>> Date: Thu, 11 Feb 2016 14:05:21 +0100
>> From: Elisa Pieri <elisa.pieri90.gmail.com>
>> Subject: Re: [AMBER] Restarting a heating simulation
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CANYcjubYjbQZ7zUVUMgHPLw595op4EqRBkWrNoDiVwoHGeihyg.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> This is the command I'm using:
>>
>> mpiexec -n 36 pmemd.MPI -O -i heat.mdin -c crys.min.rst7 -p crys.parm7
>> -cpin crys.cpin -o crys.heat.mdout -r crys.heat.rst7 -ref crys.min.rst7 -x
>> crys.heat.nc
>>
>> (so I guess it's ok). I'm using 3 nodes, 12 cores each.
>>
>> Elisa
>>
>> On Thu, Feb 11, 2016 at 2:00 PM, Jason Swails <jason.swails.gmail.com>
>> wrote:
>>
>> > On Thu, Feb 11, 2016 at 5:43 AM, Elisa Pieri <elisa.pieri90.gmail.com>
>> > wrote:
>> >
>> > > Dear all,
>> > >
>> > > I'm heating my system, but the maximum walltime in my cluster is 1 week,
>> > > that won't probably be enough. This in my current input:
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > *Implicit solvent constant pH initial heating mdin &cntrl imin=0,
>> > > irest=0, ntx=1, ntpr=500, ntwx=500, nstlim=1000000, dt=0.002,
>> > ntt=3,
>> > > tempi=10, temp0=300, tautp=2.0, ig=-1, ntp=0, ntc=2, ntf=2,
>> > > cut=30, ntb=0, igb=2, tol=0.000001, nrespa=1, saltcon=0.1,
>> > > icnstph=1, ntcnstph=100000000, gamma_ln=5.0, ntwr=500, ioutfm=1,
>> > > nmropt=1, / &wt TYPE='TEMP0', ISTEP1=1, ISTEP2=500000,
>> > VALUE1=10.0,
>> > > VALUE2=300.0, / &wt TYPE='END' /*
>> > >
>> > > First of all..my system has 3744 atoms and I'm running pmemd on 36 cores
>> > > (Intel X5675 3.06 GHz). It has an average of 10.5 minutes per picosecond,
>> > > so it will take more than two weeks to finish. Is it normal? Isn't it
>> > VERY
>> > > slow?
>> > >
>> >
>> > ?How exactly are you running in parallel? (i.e., what is the exact command
>> > that you are using?) There are a number of possible issues.
>> >
>> > A common mistake people make trying to run pmemd in parallel is to use a
>> > command that looks like
>> >
>> > mpirun -np 36 pmemd -O -i mdin ...
>> >
>> > The problem here is that pmemd (and sander) are serial executables that are
>> > incapable of parallelizing their calculation. The correct thing to do is
>> >
>> > mpirun -np 36 pmemd.MPI -O -i ...
>> >
>> > If you use pmemd instead of pmemd.MPI, then you will get the exact same
>> > performance as running on 1 CPU (perhaps worse if the CPUs are
>> > oversubscribed). It's also possible if you are asking for multiple nodes
>> > that all of the threads are running on a single node (which will slow down
>> > performance substantially). You'd have to ask your help staff to figure
>> > out if that's happening (and how to fix it), though.
>> >
>> > HTH,
>> > Jason
>> >
>> > --
>> > Jason M. Swails
>> > BioMaPS,
>> > Rutgers University
>> > Postdoctoral Researcher
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> ------------------------------
>>
>> Message: 25
>> Date: Thu, 11 Feb 2016 08:14:29 -0500
>> From: Carlos Simmerling <carlos.simmerling.gmail.com>
>> Subject: Re: [AMBER] Restarting a heating simulation
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAGk3s-RXhdcbT6AMaAxZBj9_aAQU8ECKiS+xW-VGRm1cB+uODA.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> I would suggest trying on a single node first, and then seeing if using
>> more than 1 is faster or slower.
>> On Feb 11, 2016 8:05 AM, "Elisa Pieri" <elisa.pieri90.gmail.com> wrote:
>>
>> > This is the command I'm using:
>> >
>> > mpiexec -n 36 pmemd.MPI -O -i heat.mdin -c crys.min.rst7 -p crys.parm7
>> > -cpin crys.cpin -o crys.heat.mdout -r crys.heat.rst7 -ref crys.min.rst7 -x
>> > crys.heat.nc
>> >
>> > (so I guess it's ok). I'm using 3 nodes, 12 cores each.
>> >
>> > Elisa
>> >
>> > On Thu, Feb 11, 2016 at 2:00 PM, Jason Swails <jason.swails.gmail.com>
>> > wrote:
>> >
>> > > On Thu, Feb 11, 2016 at 5:43 AM, Elisa Pieri <elisa.pieri90.gmail.com>
>> > > wrote:
>> > >
>> > > > Dear all,
>> > > >
>> > > > I'm heating my system, but the maximum walltime in my cluster is 1
>> > week,
>> > > > that won't probably be enough. This in my current input:
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > > *Implicit solvent constant pH initial heating mdin &cntrl imin=0,
>> > > > irest=0, ntx=1, ntpr=500, ntwx=500, nstlim=1000000, dt=0.002,
>> > > ntt=3,
>> > > > tempi=10, temp0=300, tautp=2.0, ig=-1, ntp=0, ntc=2, ntf=2,
>> > > > cut=30, ntb=0, igb=2, tol=0.000001, nrespa=1, saltcon=0.1,
>> > > > icnstph=1, ntcnstph=100000000, gamma_ln=5.0, ntwr=500, ioutfm=1,
>> > > > nmropt=1, / &wt TYPE='TEMP0', ISTEP1=1, ISTEP2=500000,
>> > > VALUE1=10.0,
>> > > > VALUE2=300.0, / &wt TYPE='END' /*
>> > > >
>> > > > First of all..my system has 3744 atoms and I'm running pmemd on 36
>> > cores
>> > > > (Intel X5675 3.06 GHz). It has an average of 10.5 minutes per
>> > picosecond,
>> > > > so it will take more than two weeks to finish. Is it normal? Isn't it
>> > > VERY
>> > > > slow?
>> > > >
>> > >
>> > > ?How exactly are you running in parallel? (i.e., what is the exact
>> > command
>> > > that you are using?) There are a number of possible issues.
>> > >
>> > > A common mistake people make trying to run pmemd in parallel is to use a
>> > > command that looks like
>> > >
>> > > mpirun -np 36 pmemd -O -i mdin ...
>> > >
>> > > The problem here is that pmemd (and sander) are serial executables that
>> > are
>> > > incapable of parallelizing their calculation. The correct thing to do is
>> > >
>> > > mpirun -np 36 pmemd.MPI -O -i ...
>> > >
>> > > If you use pmemd instead of pmemd.MPI, then you will get the exact same
>> > > performance as running on 1 CPU (perhaps worse if the CPUs are
>> > > oversubscribed). It's also possible if you are asking for multiple nodes
>> > > that all of the threads are running on a single node (which will slow
>> > down
>> > > performance substantially). You'd have to ask your help staff to figure
>> > > out if that's happening (and how to fix it), though.
>> > >
>> > > HTH,
>> > > Jason
>> > >
>> > > --
>> > > Jason M. Swails
>> > > BioMaPS,
>> > > Rutgers University
>> > > Postdoctoral Researcher
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> ------------------------------
>>
>> Message: 26
>> Date: Thu, 11 Feb 2016 14:37:32 +0100
>> From: Falko J?hnert <falko.jaehnert.biochemtech.uni-halle.de>
>> Subject: Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors
>> To: 'AMBER Mailing List' <amber.ambermd.org>
>> Message-ID: <001001d164d1$5eb92730$1c2b7590$.biochemtech.uni-halle.de>
>> Content-Type: text/plain; charset=utf-8
>>
>> Dear Jason,
>>
>> thanks a lot for the quick reply. So as it is a deficiency in the testing procedure it isn?t a problem for using Amber with CUDA, right? I'm not entirely sure if I understand your answer correctly. Where did this inserted lines in one of the compared files arise from? I believed this extra lines came from an alternative logging manner?
>>
>> Thanks in advance,
>> Falko J?hnert
>>
>> -----Urspr?ngliche Nachricht-----
>> Von: Jason Swails [mailto:jason.swails.gmail.com]
>> Gesendet: Donnerstag, 11. Februar 2016 14:03
>> An: AMBER Mailing List <amber.ambermd.org>
>> Betreff: Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors
>>
>> On Thu, Feb 11, 2016 at 7:36 AM, Falko J?hnert < falko.jaehnert.biochemtech.uni-halle.de> wrote:
>>
>> > Dear Amberlings,
>> >
>> >
>> >
>> > at first, thanks a lot helping me out with my last problem ?Howto
>> > cpptraj - multiple trajin-commands in one line?. @Jean-Marc Billod: I
>> > did it your way and this works just fine!
>> >
>> >
>> >
>> > Now I?ve got a little concern about the results of my installation of
>> > Amber 14. The make test-procedure at the parallel installation level
>> > (both with 2 and 4 threads) went through without a single error, even
>> > without rounding mistakes. After that i?ve compiled Amber 14 the usual
>> > way to gather CUDA-support. Now the make test produce some rounding
>> > errors which are okay (I hope), but also errors where lines one of the
>> > compared files (*.diff) are inserted and thus produce a lot of
>> > differences. If one compares the numbers of the correctly aligned
>> > lines then everything is fine (I hope ? again with some rounding
>> > errors). To understand my problem better I attached the *log- and the
>> > *.diff-files which are shortened to display only the unclear diffs.
>> >
>> >
>> >
>> > Can I ignore this diffs safely? If not, may someone provide any
>> > information handling this problem?
>> >
>>
>> ?This is a known deficiency in the CUDA testing infrastructure. All of the larger failures (i.e., that are not round-off) arise from stochastic methods (ntt=2 or ntt=3) where the random number stream is different on every GPU.
>>
>> While there is a way to fix it (and it is on the to-do list), it apparently hasn't been important enough to make it to the top yet.
>>
>> HTH,
>> Jason
>> ?
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 27
>> Date: Thu, 11 Feb 2016 08:20:04 -0700
>> From: Daniel Roe <daniel.r.roe.gmail.com>
>> Subject: Re: [AMBER] Is there a way to compare trajectories?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAAC0qOY9dL6f1MJznUghutOR6iYe=b8Lyp1Vnbdh_KADHf-qYQ.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Just to add a bit to what Carlos said, CPPTRAJ does this kind of
>> combined cluster analysis natively. You just read in your two separate
>> trajectories, and cluster on them with the 'summarysplit' and
>> 'splitframe' keywords. For example, if you have two trajectories each
>> with 1000 frames you could cluster like so:
>>
>> parm myparm.parm7
>> trajin traj1.nc
>> trajin traj2.nc
>> cluster <clustering options> summarysplit split.dat splitframe 1000
>>
>> This can be used to compare any number of trajectories.
>>
>> Another method that we have been using to compare different
>> trajectories is to calculate the Kullback-Leibler divergence to
>> quantify the overlap of various distributions calculated from each
>> trajectory - in particular the principal component projection
>> histograms. For some examples of these kinds of calculations (as well
>> as example cpptraj scripts) see these articles and their supporting
>> info:
>>
>> http://pubs.acs.org/doi/abs/10.1021/jp4125099
>> http://pubs.acs.org/doi/abs/10.1021/ct400862k
>>
>> Hope this helps,
>>
>> -Dan
>>
>> On Thu, Feb 11, 2016 at 4:27 AM, Karolina Markowska
>> <markowska.kar.gmail.com> wrote:
>> > Thank you, Carlos, that's even better!
>> >
>> > Karolina
>> >
>> > 2016-02-11 12:15 GMT+01:00 Carlos Simmerling <carlos.simmerling.gmail.com>:
>> >
>> >> We frequently read in 2 trajectories then do cluster analysis, and compare
>> >> the population of each cluster in trajectory 1 vs 2.this gives you error
>> >> bars on the population of each cluster. It's similar to 2drmsd but gives
>> >> you something more quantitative.
>> >> On Feb 11, 2016 4:27 AM, "Dr. Anselm Horn" <anselm.horn.fau.de> wrote:
>> >>
>> >> > Dear Karolina,
>> >> >
>> >> > AFAIK a 'reference' is limited to a single structure.
>> >> >
>> >> > Reading in two trajectories in a row should be no problem for cpptraj,
>> >> > as you can give several trajin commands.
>> >> > For the comparison of the two trajectories you could then use e.g. a
>> >> > 2D-RMSD-plot or perform a cluster analysis on the combined trajectories
>> >> > with a subsequent inspection of the distribution of the cluster
>> >> > structures between the trajectories. Or you could monitor some other
>> >> > properties of interest and compare those values.
>> >> >
>> >> > Regards,
>> >> >
>> >> > Anselm
>> >> >
>> >> >
>> >> > Am 11.02.2016 10:07, schrieb Karolina Markowska:
>> >> > > Dear Amber Users,
>> >> > >
>> >> > > I have two simulations with the same system and I would like to compare
>> >> > > them. Mostly I would like to check if I'm having the same protein
>> >> > > conformations in these two simulations. Does Amber software provide a
>> >> > tool
>> >> > > for that kind of analysis?
>> >> > >
>> >> > > I wanted to use cpptraj and use the first trajectory as reference, add
>> >> > the
>> >> > > second one by trajin and calculate rmsd between them, but cpptraj uses
>> >> > only
>> >> > > the first frame from that file. Can I make cpptraj to read whole
>> >> > trajectory
>> >> > > as a reference?
>> >> > > The script looked like that:
>> >> > >
>> >> > > parm protein.prmtop
>> >> > > reference sim1.nc
>> >> > > trajin sim2.nc
>> >> > > autoimage
>> >> > > strip :WAT
>> >> > > strip :Na+
>> >> > > rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass
>> >> > > quit
>> >> > >
>> >> > > | sim1.nc is the trajectory of the first simulation and sim2.nc is the
>> >> > > trajectory from the second simulation.
>> >> > >
>> >> > > Thanks for your help.
>> >> > > Best regards,
>> >> > > Karolina Markowska
>> >> > > PhD student
>> >> > > _______________________________________________
>> >> > > AMBER mailing list
>> >> > > AMBER.ambermd.org
>> >> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >> > >
>> >> > >
>> >> >
>> >> >
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>>
>>
>> ------------------------------
>>
>> Message: 28
>> Date: Thu, 11 Feb 2016 08:22:49 -0700
>> From: Daniel Roe <daniel.r.roe.gmail.com>
>> Subject: Re: [AMBER] Regarding MMGBSA calculation
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAAC0qOYbSZ3OJd4szu-Gu5QzjmW-SawtQhXY3cEzszjjQ=2XWg.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> I've seen this kind of error pop up on heterogeneous clusters with
>> Intel compilers due to the aggressive CPU-specific optimizations they
>> employ. If you want programs to be transferable between different
>> machines in such an environment you may have some luck configuring
>> with the '-nosse' flag. Otherwise just take Dave's advice and compile
>> your own local AmberTools.
>>
>> -Dan
>>
>> On Thu, Feb 11, 2016 at 3:45 AM, neha chaudhary
>> <nehachaudhary769.gmail.com> wrote:
>> > Hello Sir,
>> >
>> > I tried the command in server as /share/apps/amber/amber12/bin/cpptraj, Fatal
>> > Error: This program was not built to run in your system.
>> > Someone else installed the program on the server.
>> >
>> > Best Regards,
>> >
>> > *Neha*
>> >
>> > Research Scholar,
>> > Centre for Computational Biology and Bioinformatics,
>> > School of Life Sciences,
>> > Central University of Himachal Pradesh,
>> >
>> >
>> >
>> >
>> >
>> > On Sat, Feb 6, 2016 at 6:54 PM, David A Case <david.case.rutgers.edu> wrote:
>> >
>> >> On Sat, Feb 06, 2016, neha chaudhary wrote:
>> >> >
>> >> > I am using amber on a server, when I am runnung
>> >> /share/apps/amber/amber12/
>> >> > bin/cpptraj, Fatal Error: This program was not built to run in your
>> >> system.
>> >> > Please verify that both the operating system and the processor support
>> >> > Intel(R) AVX.
>> >>
>> >> Did you try any of the advice that Jason or I gave to your last email? (My
>> >> response is given below.) Did you install Amber yourself, or did someone
>> >> else
>> >> do it?
>> >>
>> >> ...dac
>> >>
>> >> > >
>> >> > > What happens if you type "/share/apps/amber/amber12/bin/cpptraj" at a
>> >> > > console prompt? Do the Amber test cases mostly pass?
>> >> > >
>> >> > > Related question, especially if you get failures from the previous
>> >> > > questions:
>> >> > > what OS and compiler are you using? what arguments did you give to
>> >> Amber's
>> >> > > configure script?
>> >> > >
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>>
>>
>> ------------------------------
>>
>> Message: 29
>> Date: Thu, 11 Feb 2016 07:29:26 -0800
>> From: Ross Walker <ross.rosswalker.co.uk>
>> Subject: Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <A344F081-1114-425B-ABA6-3F4058F32EB5.rosswalker.co.uk>
>> Content-Type: text/plain; charset=utf-8
>>
>> FYI This will be fixed in AMBER 16.
>>
>> For now if you are concerned you can build the DPFP model and test that:
>>
>> ./configure -cuda_DPFP gnu
>> make install
>> cd test
>> ./test_amber_cuda.sh DPFP
>>
>> The only difference here is the precision model so you get less rounding (the rest of the code is identical) so this will give you a valid test of whether things are working or not.
>>
>> Ultimately our test cases on the user pespective are way too complicated. The test suite is really designed as regression tests for those modifying the code etc while what an end user test cases need to be is one that just checks the compilation worked and tests a reasonable range of options to look for obvious compiler bugs etc. Unfortunately nobody has volunteered yet to split the testing in this way so users run the very long and complicated regression test which can lead to confusion.
>>
>> TLNR you are fine - the issue is rounding differences on different hardware - it's tricky to deal with with Newtonian integrators but the AMBER 16 approach should be more robust.
>>
>> > On Feb 11, 2016, at 05:03, Jason Swails <jason.swails.gmail.com> wrote:
>> >
>> > On Thu, Feb 11, 2016 at 7:36 AM, Falko J?hnert <
>> > falko.jaehnert.biochemtech.uni-halle.de> wrote:
>> >
>> >> Dear Amberlings,
>> >>
>> >>
>> >>
>> >> at first, thanks a lot helping me out with my last problem ?Howto cpptraj -
>> >> multiple trajin-commands in one line?. @Jean-Marc Billod: I did it your way
>> >> and this works just fine!
>> >>
>> >>
>> >>
>> >> Now I?ve got a little concern about the results of my installation of Amber
>> >> 14. The make test-procedure at the parallel installation level (both with 2
>> >> and 4 threads) went through without a single error, even without rounding
>> >> mistakes. After that i?ve compiled Amber 14 the usual way to gather
>> >> CUDA-support. Now the make test produce some rounding errors which are okay
>> >> (I hope), but also errors where lines one of the compared files (*.diff)
>> >> are
>> >> inserted and thus produce a lot of differences. If one compares the numbers
>> >> of the correctly aligned lines then everything is fine (I hope ? again with
>> >> some rounding errors). To understand my problem better I attached the *log-
>> >> and the *.diff-files which are shortened to display only the unclear diffs.
>> >>
>> >>
>> >>
>> >> Can I ignore this diffs safely? If not, may someone provide any information
>> >> handling this problem?
>> >>
>> >
>> > ?This is a known deficiency in the CUDA testing infrastructure. All of the
>> > larger failures (i.e., that are not round-off) arise from stochastic
>> > methods (ntt=2 or ntt=3) where the random number stream is different on
>> > every GPU.
>> >
>> > While there is a way to fix it (and it is on the to-do list), it apparently
>> > hasn't been important enough to make it to the top yet.
>> >
>> > HTH,
>> > Jason
>> > ?
>> > --
>> > Jason M. Swails
>> > BioMaPS,
>> > Rutgers University
>> > Postdoctoral Researcher
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 30
>> Date: Thu, 11 Feb 2016 07:31:54 -0800
>> From: Ross Walker <ross.rosswalker.co.uk>
>> Subject: Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <FC344A9B-F62B-4F5D-9358-D8C1183644AD.rosswalker.co.uk>
>> Content-Type: text/plain; charset=utf-8
>>
>> Actually, looking more closely, the main failures shown here are all for IGB=8. This is because update.12 changed the GBNeck2 parameters and thus all IGB=8 results:
>>
>> http://ambermd.org/bugfixes/14.0/update.12
>>
>> It did not however update the test cases. So in this case the test suite is correct - IGB8 is now, as far as the test suite is concerned, giving incorrect answers. The IGB8 test output needs to be updated and the author of update.12 should make an additional update to fix this.
>>
>> All the best
>> Ross
>>
>> > On Feb 11, 2016, at 05:03, Jason Swails <jason.swails.gmail.com> wrote:
>> >
>> > On Thu, Feb 11, 2016 at 7:36 AM, Falko J?hnert <
>> > falko.jaehnert.biochemtech.uni-halle.de> wrote:
>> >
>> >> Dear Amberlings,
>> >>
>> >>
>> >>
>> >> at first, thanks a lot helping me out with my last problem ?Howto cpptraj -
>> >> multiple trajin-commands in one line?. @Jean-Marc Billod: I did it your way
>> >> and this works just fine!
>> >>
>> >>
>> >>
>> >> Now I?ve got a little concern about the results of my installation of Amber
>> >> 14. The make test-procedure at the parallel installation level (both with 2
>> >> and 4 threads) went through without a single error, even without rounding
>> >> mistakes. After that i?ve compiled Amber 14 the usual way to gather
>> >> CUDA-support. Now the make test produce some rounding errors which are okay
>> >> (I hope), but also errors where lines one of the compared files (*.diff)
>> >> are
>> >> inserted and thus produce a lot of differences. If one compares the numbers
>> >> of the correctly aligned lines then everything is fine (I hope ? again with
>> >> some rounding errors). To understand my problem better I attached the *log-
>> >> and the *.diff-files which are shortened to display only the unclear diffs.
>> >>
>> >>
>> >>
>> >> Can I ignore this diffs safely? If not, may someone provide any information
>> >> handling this problem?
>> >>
>> >
>> > ?This is a known deficiency in the CUDA testing infrastructure. All of the
>> > larger failures (i.e., that are not round-off) arise from stochastic
>> > methods (ntt=2 or ntt=3) where the random number stream is different on
>> > every GPU.
>> >
>> > While there is a way to fix it (and it is on the to-do list), it apparently
>> > hasn't been important enough to make it to the top yet.
>> >
>> > HTH,
>> > Jason
>> > ?
>> > --
>> > Jason M. Swails
>> > BioMaPS,
>> > Rutgers University
>> > Postdoctoral Researcher
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 31
>> Date: Thu, 11 Feb 2016 15:34:56 +0000
>> From: "Aronica, Pietro" <pietro.aronica07.imperial.ac.uk>
>> Subject: [AMBER] Quasi-harmonic Calculations
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <VI1PR06MB1037CFA215F53FCA655084D4A4A80.VI1PR06MB1037.eurprd06.prod.outlook.com>
>>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hello,
>> I wanted to perform quasi-harmonic calculations of an interaction I have to estimate the entropy. I have been told that in order for this to work properly, the simulation needs to be of at least a certain length. I've also been told that this issue had been discussed on the mailing list before, but I have failed to find relevant information, just hints, and the tutorials are rather vague on the subject. Where can I find exact information on how quasi-harmonic calculations ought to be run?
>> Cheers
>> Pietro
>>
>> ------------------------------
>>
>> Message: 32
>> Date: Thu, 11 Feb 2016 15:40:50 +0000
>> From: "Osman, Roman" <roman.osman.mssm.edu>
>> Subject: Re: [AMBER] Is there a way to compare trajectories?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <251B001D-4C01-4DBB-98D8-83D9B158C37B.mssm.edu>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Karolyn's
>> My colleague Mihaly Mezei implemented a 2D rmsd comparison of two trajectories.
>> Please contact him. Mihaly.mezei.mssm.edu
>>
>> I used it and it's a great tool
>>
>> Roman Osman
>> Sent from my iPhone
>>
>> > On Feb 11, 2016, at 4:45 AM, Karolina Markowska <markowska.kar.gmail.com> wrote:
>> >
>> > Thank you, Bill and Anselm for your advices,
>> >
>> > I think I will try the 2D-RMSD-plot first.
>> >
>> > Have a nice day!
>> > Karolina
>> >
>> > 2016-02-11 10:27 GMT+01:00 Dr. Anselm Horn <anselm.horn.fau.de>:
>> >
>> >> Dear Karolina,
>> >>
>> >> AFAIK a 'reference' is limited to a single structure.
>> >>
>> >> Reading in two trajectories in a row should be no problem for cpptraj,
>> >> as you can give several trajin commands.
>> >> For the comparison of the two trajectories you could then use e.g. a
>> >> 2D-RMSD-plot or perform a cluster analysis on the combined trajectories
>> >> with a subsequent inspection of the distribution of the cluster
>> >> structures between the trajectories. Or you could monitor some other
>> >> properties of interest and compare those values.
>> >>
>> >> Regards,
>> >>
>> >> Anselm
>> >>
>> >>
>> >> Am 11.02.2016 10:07, schrieb Karolina Markowska:
>> >>> Dear Amber Users,
>> >>>
>> >>> I have two simulations with the same system and I would like to compare
>> >>> them. Mostly I would like to check if I'm having the same protein
>> >>> conformations in these two simulations. Does Amber software provide a
>> >> tool
>> >>> for that kind of analysis?
>> >>>
>> >>> I wanted to use cpptraj and use the first trajectory as reference, add
>> >> the
>> >>> second one by trajin and calculate rmsd between them, but cpptraj uses
>> >> only
>> >>> the first frame from that file. Can I make cpptraj to read whole
>> >> trajectory
>> >>> as a reference?
>> >>> The script looked like that:
>> >>>
>> >>> parm protein.prmtop
>> >>> reference sim1.nc
>> >>> trajin sim2.nc
>> >>> autoimage
>> >>> strip :WAT
>> >>> strip :Na+
>> >>> rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass
>> >>> quit
>> >>>
>> >>> | sim1.nc is the trajectory of the first simulation and sim2.nc is the
>> >>> trajectory from the second simulation.
>> >>>
>> >>> Thanks for your help.
>> >>> Best regards,
>> >>> Karolina Markowska
>> >>> PhD student
>> >>> _______________________________________________
>> >>> AMBER mailing list
>> >>> AMBER.ambermd.org
>> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=AwICAg&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=KGmK9QeuQGXU7AfWRng1JopBHi5t89pb6Jler12nUVM&s=5BH1TxzxAz0WEJlWLjovtEOPmgsq-547ySiRojtBe6U&e=
>> >>
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=AwICAg&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=KGmK9QeuQGXU7AfWRng1JopBHi5t89pb6Jler12nUVM&s=5BH1TxzxAz0WEJlWLjovtEOPmgsq-547ySiRojtBe6U&e=
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=AwICAg&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=KGmK9QeuQGXU7AfWRng1JopBHi5t89pb6Jler12nUVM&s=5BH1TxzxAz0WEJlWLjovtEOPmgsq-547ySiRojtBe6U&e=
>>
>>
>>
>> ------------------------------
>>
>> Message: 33
>> Date: Thu, 11 Feb 2016 11:04:12 -0500
>> From: Jason Swails <jason.swails.gmail.com>
>> Subject: Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAEk9e3q2pOm-OJxZ6763Tx6uE0fH6ONby-uR=KBatbKk0M=ofA.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> On Thu, Feb 11, 2016 at 10:31 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
>>
>> > Actually, looking more closely, the main failures shown here are all for
>> > IGB=8. This is because update.12 changed the GBNeck2 parameters and thus
>> > all IGB=8 results:
>> >
>> > http://ambermd.org/bugfixes/14.0/update.12
>> >
>> > It did not however update the test cases. So in this case the test suite
>> > is correct - IGB8 is now, as far as the test suite is concerned, giving
>> > incorrect answers. The IGB8 test output needs to be updated and the author
>> > of update.12 should make an additional update to fix this.
>> >
>>
>> ?The results are the same, but the output info in the header is
>> mismatched. But since I fixed all your Makefile stuff with pmemd.cuda,
>> I'll let you handle the CUDA test update if you want it fixed ;).
>>
>> -Jason
>> ?
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> ------------------------------
>>
>> Message: 34
>> Date: Thu, 11 Feb 2016 11:42:57 -0500
>> From: Jason Swails <jason.swails.gmail.com>
>> Subject: Re: [AMBER] Quasi-harmonic Calculations
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAEk9e3pc9xJ2ZtCSSQa7EPoZeyV+8=uxUb4Wti9+8P8zO83osQ.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> On Thu, Feb 11, 2016 at 10:34 AM, Aronica, Pietro <
>> pietro.aronica07.imperial.ac.uk> wrote:
>>
>> > Hello,
>> > I wanted to perform quasi-harmonic calculations of an interaction I have
>> > to estimate the entropy. I have been told that in order for this to work
>> > properly, the simulation needs to be of at least a certain length. I've
>> > also been told that this issue had been discussed on the mailing list
>> > before, but I have failed to find relevant information, just hints, and the
>> > tutorials are rather vague on the subject. Where can I find exact
>> > information on how quasi-harmonic calculations ought to be run?
>> >
>>
>> ?Journal articles. There seem to be some promising hits on Google Scholar:
>> https://scholar.google.com/scholar?hl=en&q=quasi-harmonic+entropy&btnG=&as_sdt=1%2C5&as_sdtp=
>>
>> It may also take some amount of "try it and see" (e.g., in terms of how
>> many frames to include, etc.).
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> ------------------------------
>>
>> Message: 35
>> Date: Thu, 11 Feb 2016 11:57:39 -0500
>> From: kaushik chakraborty <kaushik290187.gmail.com>
>> Subject: [AMBER] Unable to run QM/MM with RNA and sodium ion
>> To: amber.ambermd.org
>> Message-ID:
>> <CAK=ChW93K5LYMsxM+y35KKf22jCruGiE-ALBjQ6Mfkv-OhvgVw.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear All,
>>
>> I was trying to perform qm/mm simulation of a RNA molecule using CHARMM
>> forcefield
>> in amber 12. It was running fine when I there is only RNA atoms within the
>> QM region.
>> But as I consider one Na+ ion along with RNA atoms within the QM region it
>> was showing that
>> "Unable to correctly identify element SOD".
>>
>> Could you please help me or give me any advice about this error?
>> Thanks in advance!
>>
>> Kaushik
>>
>>
>> ------------------------------
>>
>> Message: 36
>> Date: Thu, 11 Feb 2016 10:20:48 -0700
>> From: Daniel Roe <daniel.r.roe.gmail.com>
>> Subject: Re: [AMBER] Quasi-harmonic Calculations
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAAC0qOYxSOS0L8n-FXG_gGPOzs9h-=jAS5fNNxx+Mqxkyjz1Mg.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Hi,
>>
>> Just to add to what Jason said, just to even properly populate your
>> mass-weighted covariance matrix you will need at least as many frames
>> as you have rows (i.e. N = # atoms in your covariance matrix times 3).
>> For a good estimate of the entropy I suspect you'll probably want at
>> least 10 times that, although I'm sure some of the articles Jason
>> pointed out have better recommendations. One measure you can use is to
>> perform your quasi-harmonic calculation, then extend your simulations
>> by N frames and observe how your calculated values change.
>>
>> -Dan
>>
>> On Thu, Feb 11, 2016 at 9:42 AM, Jason Swails <jason.swails.gmail.com> wrote:
>> > On Thu, Feb 11, 2016 at 10:34 AM, Aronica, Pietro <
>> > pietro.aronica07.imperial.ac.uk> wrote:
>> >
>> >> Hello,
>> >> I wanted to perform quasi-harmonic calculations of an interaction I have
>> >> to estimate the entropy. I have been told that in order for this to work
>> >> properly, the simulation needs to be of at least a certain length. I've
>> >> also been told that this issue had been discussed on the mailing list
>> >> before, but I have failed to find relevant information, just hints, and the
>> >> tutorials are rather vague on the subject. Where can I find exact
>> >> information on how quasi-harmonic calculations ought to be run?
>> >>
>> >
>> > Journal articles. There seem to be some promising hits on Google Scholar:
>> > https://scholar.google.com/scholar?hl=en&q=quasi-harmonic+entropy&btnG=&as_sdt=1%2C5&as_sdtp=
>> >
>> > It may also take some amount of "try it and see" (e.g., in terms of how
>> > many frames to include, etc.).
>> >
>> > HTH,
>> > Jason
>> >
>> > --
>> > Jason M. Swails
>> > BioMaPS,
>> > Rutgers University
>> > Postdoctoral Researcher
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>>
>>
>> ------------------------------
>>
>> Message: 37
>> Date: Thu, 11 Feb 2016 11:27:08 -0600
>> From: Carlos Romero <carlos.rom.74he.gmail.com>
>> Subject: [AMBER] interpret results
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAA_maK2+kQuKzrRwkj=iG4nBrge1AwzuFkHf-pvnUZGg+sEY8Q.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Hi dear all.
>>
>> I am working in protein interactions en presence of ions. I make
>> simulations according to AMBER tutorials.
>>
>> The procedure I follow is the next:
>>
>> When I have a complex, I separate receptor and ligand with a text editor.
>> I add ions, solvate, do minimizations, heating and Dynamic simulations
>> according to Tutorials.
>>
>> When the dynamics finish, normally I get a PDB file by ampbdb utility from
>> both molecules, receptor and ligands, and I make a docking using Hex 6.3.
>>
>> It is the way I thought I could observe a conformational change in both
>> molecules and see if in presence of ions have the same behavior.
>>
>> But I was looking in literature if this procedure was correct and I found
>> that the way of analyse the results is diferent.
>>
>> My question is: could anybody help me in suggets literature for what means
>> a dinamyc molecular simulation?, and how can I interpret results?
>>
>> I searched in the internet but it is a lot of information and I really
>> don't understand so much.
>>
>> I appreciate your comments.
>>
>>
>> Regards
>>
>>
>> ------------------------------
>>
>> Message: 38
>> Date: Thu, 11 Feb 2016 20:56:50 +0100
>> From: Batuhan Kav <bkav13.ku.edu.tr>
>> Subject: [AMBER] Error: Bad > topology file.
>> To: amber.ambermd.org
>> Message-ID: <D1FB6DE5-0074-486D-8FB8-32A5D336FEAC.ku.edu.tr>
>> Content-Type: text/plain; charset=utf-8
>>
>> Dear All,
>>
>> I am simulating a system of two sugar molecules in water box. I obtain the structure from glycam website, and bind monosaccharides using bond command in tleap. When running equilibration run, a faced with the error ?Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM?. Interestingly (for me, at least), both minimization and heating runs did not give any errors, although I am using sander.MPI for all pre-production runs.
>>
>> I know this is a known bug in tleap, and also know how to fix it. I wanted to ask if it would be safe to think that bond command worked correctly when I do not get any ?bad topology? errors.
>>
>> With the same bond commands in tleap I have created many systems, and this is the first time that I got such an error.
>>
>> I use AmberTools15, if it helps.
>>
>> Best,
>> Batuhan
>>
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> End of AMBER Digest, Vol 1483, Issue 1
>> **************************************
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 11 2016 - 22:30:04 PST
