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:
>
> >NSTEPENERGY 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.
>
>
>
>
>
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>
> ------------------------------
>
> 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>
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>
> 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
>
>
>
>
> ------------------------------
>
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>
> End of AMBER Digest, Vol 1483, Issue 1
> **************************************
>
>
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Received on Thu Feb 11 2016 - 21:30:06 PST
