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-- *Regards* Garima Singh AcSIR-PhD Fellow Biotechnology Division C/o Dr. Ashok Sharma (Chief Scientist and Head Biotechnology Division) Central Institute Of Medicinal And Aromatic Plant CSIR-CIMAP Lucknow garimabioinfo.gmail.com *INDIA* Please don't print this e-mail unless you really need to. Be Green ! On Fri, Jun 23, 2017 at 12:30 AM, <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: "Abort trap 6" error message with tLeap and xLeap > (Xichong Liu) > 2. Re: Duplicate random seeds with ig=-1 Code enhancement to > think about, perhaps (Chris Moth) > 3. Re: Leap: Periodic Boundary of DNA (David Case) > 4. correlated dihedrals in ff parameterization (Bala subramanian) > 5. Amber md in HPC : Job terminated (Garima Singh) > 6. Re: correlated dihedrals in ff parameterization (Karl Kirschner) > 7. Re: Amber md in HPC : Job terminated (Elvis Martis) > 8. Re: Amber md in HPC : Job terminated (David A Case) > 9. Problem Imaging atoms of system crossing the PBC box from > opposite faces of box at the same time (SHAILESH KUMAR) > 10. Re: Problem Imaging atoms of system crossing the PBC box from > opposite faces of box at the same time (Daniel Roe) > 11. Re: Problem Imaging atoms of system crossing the PBC box from > opposite faces of box at the same time (SHAILESH KUMAR) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 21 Jun 2017 22:53:23 +0200 > From: Xichong Liu <xichongl.princeton.edu> > Subject: Re: [AMBER] "Abort trap 6" error message with tLeap and xLeap > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: <DAF83E37-630C-43F8-9566-3DB4510A5E19.princeton.edu> > Content-Type: text/plain; charset=utf-8 > > Dear Hai and David: > > Thanks so much for your response! I think the clang compiler was the > issue. I did ?make distclean? to uninstall AmberTools17 and removed the > entire directory and then did what Hai suggested. After reinstallation, > tLeap seems to be exporting the files successfully now! > > Thanks again! > > Best, > > Andy Liu > > On Jun 21, 2017, at 4:37 PM, Hai Nguyen <nhai.qn.gmail.com> wrote: > > > > hi, you can try either > > > > - install binary distribution > > - If you already installed suggested gfortran (amber website), you can > > switch to GNU compiler > > export CC=/usr/local/gfortran/bin/gcc > > export CXX=/usr/local/gfortran/bin/g++ > > > > ./configure gnu > > > > (or set CC and CXX to your installed GNU compiler) > > > > .Dave: I got similar issue with tleap, macos+clang on my mac for > amber-dev > > too (reported). > > > > Hai > > > > > > On Wed, Jun 21, 2017 at 9:53 AM, Xichong Liu <xichongl.princeton.edu> > wrote: > > > >> Hi David: > >> > >> I used ./configure clang -macAccelerate for the configure script during > >> the installation. ?Which gcc? gives ?/usr/bin/gcc? and ?gcc -v? gives: > >> > >> Configured with: --prefix=/Library/Developer/CommandLineTools/usr > >> --with-gxx-include-dir=/usr/include/c++/4.2.1 > >> Apple LLVM version 8.1.0 (clang-802.0.42) > >> Target: x86_64-apple-darwin16.6.0 > >> Thread model: posix > >> InstalledDir: /Library/Developer/CommandLineTools/usr/bin > >> > >> After running configure with -debug option, the same error messages > >> remained and no new information was generated. I?m not sure if this is > >> specific for AmberTools17 because it?s the only one I have installed. I > >> could try using a different version later. The MacOS I?m using is Sierra > >> 10.12.5. > >> > >> Thanks for the help! > >> > >> Andy Liu > >> > >> > >>> On Jun 21, 2017, at 2:45 PM, David A Case <david.case.rutgers.edu> > >> wrote: > >>> > >>> On Wed, Jun 21, 2017, Xichong Liu wrote: > >>>> > >>>> I have recently installed AmberTools17 on my personal MacBook and ran > >>>> into some issues with Leap. > >>> > >>> Thanks for the report. What options did you give to the configure > >> script? > >>> What is the result of the commands "which gcc" and "gcc -v"? Finally, > >>> what version of MacOS are you using? > >>> > >>> This sounds like a tough thing to debug until someone else has a > machine > >>> on which the tleap tests fail in this manner. You can try this: > >>> > >>> Re-run configure with the "-debug" option; recompile; then see what > >> happens > >>> on one of the tleap test cases. It may work then; or you may get more > >>> information; or you may not learn anything useful. > >>> > >>> (Aside: do you know if this is specific to AmberTools17? That is, have > >>> you run an earlier version of AmberTools using this machine and > >> compilers?) > >>> > >>> ...dac > >>> > >>> > >>> _______________________________________________ > >>> 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: 2 > Date: Wed, 21 Jun 2017 16:37:43 -0500 > From: Chris Moth <cmoth08.gmail.com> > Subject: Re: [AMBER] Duplicate random seeds with ig=-1 Code > enhancement to think about, perhaps > To: AMBER Mailing List <amber.ambermd.org>, Daniel Roe > <daniel.r.roe.gmail.com> > Message-ID: <5e5df6e8-739b-f1e9-1b01-87728282725a.gmail.com> > Content-Type: text/plain; charset=utf-8; format=flowed > > "Setting ig manually" was on the original menu I proposed. That seems > reasonable to me. The only "problem" is that our tutorials somewhat > claim, implicitly, that "ig=-1" is an option you can specify safely, and > not have to think about it again. > > Guids are very effective in my commercial coding experience - but 128 > bit strings - not 31 (which I continue to hope is the correct bit-count > of these seeds, if not 32) And, they require linking to libraries that > may not be quite "standard enough" for the culture of AMBER. > > For now, I have "solved" my problem on our platform by sleeping > "RunSubscript" (0-99) seconds before start of each of the 100 runs. I > carefully check for duplicate runs on completion of each stage now. So > far, so good. > > Adding another 10 bits of entropy from /dev/urandom to the 20 bits from > the microsceonds, still strikes me as a nice "to do" for the next major > AMBER release. > > As final geek-out, I'll leave you with a silly mathematical "proof" of > the problem :) (Apologies if this went out already - but I am not > seeing it in any replies). > > Like birthdays, the microseconds are uniformly distributed :) At least, > I found that if you repeatedly call gettimeofday() (and nothing else), > and stuff the results in an array, you get back all the contiguous > microseconds on fast hardware :) (which contradicts the lower time > resolution that the google hits reported from a few years ago). > > The "proof" :) > > Following the math at this site - which seems right: > > https://betterexplained.com/articles/understanding-the-birthday-paradox/ > <https://betterexplained.com/articles/understanding-the-birthday-paradox/> > > It is helpful to restate the familiar birthdays phenomenon first: > > With 23 people in a room there are 253 possible pairs of people in the > room: (23 x 22 / 2) = 253 > > Chance of 2 people having different birthdays: (1 - 1/365) = (364/365) > > Probably of making 253 comparisons and seeing all paris have different > birthdayis (364 / 365) ^ 253 -> . probability of 0.4995 > > > Jobs on the cluster next: > > Extending the same math to 100 jobs with 1000000 randomly distributed > microsecond start times :) > > With 100 jobs there are (100 * 99 / 2) = 4950 possible pairs > > Chance of 2 jobs having same microsecond assignment = (1-1/1000000) = > (999999/1000000) > > Making 4950 comparisons and have them all be different is > (999999/1000000) ^ 4950 = .9951 > > OK - oops - it is 1 in 200 batch submissions of (100 jobs) that should > see a duplicate microsecond assignment :) But still....... > > And, if the scheduler (quite plausibly) launches them all in 1/100 of a > second (which ours does not... yet) the picture gets 100x worse for > duplicate random seeds: > > (99999/100000)^4950 = .952 (1 in 20 of the 100-job batch submissions > should have a duplicate random seed) > > With the current algorithm, this tiny/silly/nuisance problem should only > get "worse" as hardware improves, more parallel runs are requested, and > their start times cluster closer and closer together on clusters. > > OK - back to real work :) > > > > > > > On 6/21/2017 7:42 AM, Daniel Roe wrote: > > One last option that I don't think has been mentioned yet: if you > > absolutely want to make sure you use a different random seed for > > multiple jobs you can always set 'ig' manually for each one according > > to whatever scheme you like. > > > > -Dan > > > > On Tue, Jun 20, 2017 at 7:41 PM, Bill Ross <ross.cgl.ucsf.edu> wrote: > >>> Another way to guarantee uniqueness is serialize access to a generator > at startup, which could be on one node. > >> Or you could have a voting scheme that would harvest the entropy between > >> the nodes (but still produce seeds serially). > >> > >> Bill > >> > >> On 6/20/17 1:55 PM, Bill Ross wrote: > >>> > https://www.guidgenerator.com/ > >>> > >>> Oops, I spoke too soon, I assumed they were guaranteed to be unique. > >>> > >>> Another way to guarantee uniqueness is serialize access to a generator > >>> at startup, which could be on one node. > >>> > >>> Bill > >>> > >>> > >>> On 6/20/17 1:50 PM, Bill Ross wrote: > >>>>> we set up a web server that keeps a list of all seeds that have ever > been used for any Amber simulation > >>>> Good idea, done in a general way here: > >>>> > >>>> https://www.guidgenerator.com/ > >>>> > >>>> Bill > >>>> > >>>> On 6/20/17 1:20 PM, David Case wrote: > >>>>> On Tue, Jun 20, 2017, Adrian Roitberg wrote: > >>>>> > >>>>>> One can, but again, that is system dependent, so we do not want to > >>>>>> depend on that. > >>>>> I'm lost here: we expect the results for ig=-1 to be system > dependent, since > >>>>> surely gettimeofday() is implemented in different ways on different > hardware. > >>>>> > >>>>> The key design goal is not to end up with duplicate seeds; once you > have a > >>>>> seed, it gets printed in the output file, and you can use that to > re-run the > >>>>> job if needed. > >>>>> > >>>>> But whether or not the particular seed chosen is system dependent or > not seems > >>>>> irrelevant(?) > >>>>> > >>>>> Here's my idea: we set up a web server that keeps a list of all > seeds that > >>>>> have ever been used for any Amber simulation. Then pmemd can > interrogate that > >>>>> database at startup, and make sure that it is using a seed that has > never been > >>>>> used before. > >>>>> > >>>>> ....dac > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> 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 > > > > > > > > ------------------------------ > > Message: 3 > Date: Wed, 21 Jun 2017 20:52:43 -0400 > From: David Case <david.case.rutgers.edu> > Subject: Re: [AMBER] Leap: Periodic Boundary of DNA > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: <20170622005243.o2fl546n4v3cygbh.scarletmail.rutgers.edu> > Content-Type: text/plain; charset=us-ascii > > On Wed, Jun 21, 2017, Johannes Kalliauer wrote: > > > > I would like to use periodic boundary-conditions of DNA (infinite long > DNA), > > therefore the molecule has bounds beyond the boundary. > > Amber doesn't support this sort of periodicity; specifically, you can't > have > bonds across periodic boundaries. > > ....dac > > > > > ------------------------------ > > Message: 4 > Date: Thu, 22 Jun 2017 10:42:58 +0200 > From: Bala subramanian <bala.biophysics.gmail.com> > Subject: [AMBER] correlated dihedrals in ff parameterization > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CA+WPOVPH5rrHiknOJ6cA9f9f58=NsCNZ_saeAr4YbgqSvMniDg.mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear Amber users, > > I am doing ff parameterization for a molecule (a amino acid mimic), where > QM optimized energies of a dihedral scan vary depending on torsions of > another dihedral, which facilitates intramolecular hbond. > > I assume that in ff parameteriztion each dihedral is considered independent > of others while deriving the torsional term. I would like to know any > caution/suggestion from field experts how correlated dihedrals can/should > be treated to obtain the torsional terms. > > I apologize if this query is more general and not specifically about any > Amber code. > > Thanks, > > Bala > > > ------------------------------ > > Message: 5 > Date: Thu, 22 Jun 2017 15:56:49 +0530 > From: Garima Singh <garimabioinfo.gmail.com> > Subject: [AMBER] Amber md in HPC : Job terminated > To: amber.ambermd.org > Message-ID: > <CAD=mwY2MMi2EtB_jwnyF4L5WuEg=a0KD29VE9Oi=bu-FUCDv8g.mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear amber user > > I am new HPC user running the md using Amber14 > .JOB was terminate giving this msg in job output file > > Warning: no access to tty (Bad file descriptor). > Thus no job control in this shell. > ***** Processor 49 > ***** System must be very inhomogeneous. > ***** Readjusting recip sizes. > In this slab, Atoms found: 1163 Allocated: 1152 > > ***** Processor 38 > ***** System must be very inhomogeneous. > ***** Readjusting recip sizes. > In this slab, Atoms found: 1156 Allocated: 1152 > > ***** Processor 39 > ***** System must be very inhomogeneous. > ***** Readjusting recip sizes. > In this slab, Atoms found: 1173 Allocated: 1152 > > ***** Processor 40 > ***** System must be very inhomogeneous. > ***** Readjusting recip sizes. > In this slab, Atoms found: 1213 Allocated: 1152 > > > here is my pbs script for run > > #!/bin/csh > #PBS -l walltime=48:00:00 > #PBS -N my_job > #PBS -q workq > #PBS -l select=16:ncpus=16:mpiprocs=16 > #PBS -l place=scatter:excl > #PBS -V > > > # Go to the directory from which you submitted the job > cd $PBS_O_WORKDIR > > source /usr/share/Modules/init/csh > setenv MPI_DEBUG "all" > setenv MPI_IB_RAILS "2" > setenv MPI_DSM_DISTRIBUTE "1" > setenv MPI_VERBOSE "1" > setenv MPI_BUFS_THRESHOLD "1" > setenv MPI_BUFS_PER_PROC "1024" > > > source /home/ashoks/amber14/amber14/amber.csh > > module load amber14 > > > module load intel-cluster-studio-2013-sp1 > > cd /home/ashoks/5_garima/pm/pm > mpirun -np 256 sander.MPI -O -i Prod.in -o Prod.out -p cd_cdpm7.prmtop -c > Hat.rst -r prod.rst -x prod.mdcrd -inf prod.info > > What is the problem i could not understand kindly provide your valuable > suggestion to overcome this issue? > > > > *Thank You and Best Wishes* > -- > *Regards* > Garima Singh > AcSIR-PhD Fellow > Biotechnology Division > C/o Dr. Ashok Sharma (Chief Scientist and Head Biotechnology Division) > Central Institute Of Medicinal And Aromatic Plant > CSIR-CIMAP > Lucknow > garimabioinfo.gmail.com > > > > > *INDIA* Please don't print this e-mail unless you really need to. Be Green > ! > > > ------------------------------ > > Message: 6 > Date: Thu, 22 Jun 2017 12:40:20 +0200 > From: Karl Kirschner <k.n.kirschner.gmail.com> > Subject: Re: [AMBER] correlated dihedrals in ff parameterization > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAF=D-bzpHq5sUs3MMbOUa-tk7WTdrmz1muZbuKxkUtkqRnmTfQ. > mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hello Bala, > > You are correct - traditionally dihedrals are considered independent with > respect to other internal coordinates when one does parameter optimization. > When you have a molecule that can form an intramolecular hydrogen bond, you > want to generate conformations, during a rotational scan of the dihedral, > such that the intramolecular hydrogen bond is disallowed. (Note, that I am > assuming that we are talking about an intrammolecular hydrogen bond that is > formed or broken during to the dihedral rotation, versus one that is remote > from the torsion of interest.) An example of this is in the optimization of > carbohydrate parameters (eg. Glycam06 and O-C5-C6-O5). The can often be > accomplished by putting the hydroxyl hydrogen into a trans conformation. > Sometimes you will also need to put a second constraint in your QM and MM > optimizations to prohibit the hydroxyl rotation. This can be conceptually > rationalized by considering what happens to a solute molecule in a hydrated > phase - most often the water will compete with the solute's intramolecular > forces to form an intermolecular hydrogen bond, and thus you underlying > solute potential energy needs to reflect that in some way. > > So all of that are for Class I force fields, like Amber's. However, in > Class II force fields, you have cross terms that can explicitly account for > the coupling between internal coordinates. These can take the form of > bond-angle, angle-torsion, torsion-torsion, etc. terms. These extra terms > in the force-field equation add additional costs for calculating the > forces, but they are also tend to be more accurate. Allinger's MM4 program > is a good example of a Class II force field that achieves very high > accuracy. > > I would suggest to do some addtional reading - a quick search gave me > this recent paper that is informative: > > Vanommeslaeghe, K., Guvench, O., & MacKerell, A. D. (2014). Molecular > Mechanics. *Current Pharmaceutical Design*, *20*(20), 3281?3292. > > Hope that helps, > Karl > > Karl. N. Kirschner, Ph.D. > Research Associate > Bonn-Rhein-Sieg University of Applied Sciences > Grantham-Allee 20, 54757 Sankt Augustin, Germany > Twitter: .k_n_kirschner <https://twitter.com/k_n_kirschner> > > On Thu, Jun 22, 2017 at 10:42 AM, Bala subramanian < > bala.biophysics.gmail.com> wrote: > > > Dear Amber users, > > > > I am doing ff parameterization for a molecule (a amino acid mimic), where > > QM optimized energies of a dihedral scan vary depending on torsions of > > another dihedral, which facilitates intramolecular hbond. > > > > I assume that in ff parameteriztion each dihedral is considered > independent > > of others while deriving the torsional term. I would like to know any > > caution/suggestion from field experts how correlated dihedrals can/should > > be treated to obtain the torsional terms. > > > > I apologize if this query is more general and not specifically about any > > Amber code. > > > > Thanks, > > > > Bala > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 7 > Date: Thu, 22 Jun 2017 11:35:59 +0000 > From: "Elvis Martis" <elvis.martis.bcp.edu.in> > Subject: Re: [AMBER] Amber md in HPC : Job terminated > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <MAXPR01MB02182BD4EA8FC768AA3D8C73A3DB0.MAXPR01MB0218. > INDPRD01.PROD.OUTLOOK.COM> > > Content-Type: text/plain; charset="us-ascii" > > Hi, > > Your systems seems inhomogeneous because there could be vacuum in your > system. > > How did you equilibrate the system and after how long do you get this > error? > > > Best Regards > > [photo] > > > > Elvis Martis > Ph.D. Student (Computational Chemistry) > at Bombay College of Pharmacy > > > A Kalina, Santacruz [E], Mumbai 400098, INDIA > W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in> > Skype. adrian_elvis12<https://webapp.wisestamp.com/#> > > > [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT- > ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_ > yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0- > d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/ > icons_for_colors_32/linkedin.png]<http://www.linkedin.com/ > in/elvisadrianmartis/> > > > > > > ________________________________ > From: Garima Singh <garimabioinfo.gmail.com> > Sent: 22 June 2017 15:56:49 > To: amber.ambermd.org > Subject: [AMBER] Amber md in HPC : Job terminated > > Dear amber user > > I am new HPC user running the md using Amber14 > .JOB was terminate giving this msg in job output file > > Warning: no access to tty (Bad file descriptor). > Thus no job control in this shell. > ***** Processor 49 > ***** System must be very inhomogeneous. > ***** Readjusting recip sizes. > In this slab, Atoms found: 1163 Allocated: 1152 > > ***** Processor 38 > ***** System must be very inhomogeneous. > ***** Readjusting recip sizes. > In this slab, Atoms found: 1156 Allocated: 1152 > > ***** Processor 39 > ***** System must be very inhomogeneous. > ***** Readjusting recip sizes. > In this slab, Atoms found: 1173 Allocated: 1152 > > ***** Processor 40 > ***** System must be very inhomogeneous. > ***** Readjusting recip sizes. > In this slab, Atoms found: 1213 Allocated: 1152 > > > here is my pbs script for run > > #!/bin/csh > #PBS -l walltime=48:00:00 > #PBS -N my_job > #PBS -q workq > #PBS -l select=16:ncpus=16:mpiprocs=16 > #PBS -l place=scatter:excl > #PBS -V > > > # Go to the directory from which you submitted the job > cd $PBS_O_WORKDIR > > source /usr/share/Modules/init/csh > setenv MPI_DEBUG "all" > setenv MPI_IB_RAILS "2" > setenv MPI_DSM_DISTRIBUTE "1" > setenv MPI_VERBOSE "1" > setenv MPI_BUFS_THRESHOLD "1" > setenv MPI_BUFS_PER_PROC "1024" > > > source /home/ashoks/amber14/amber14/amber.csh > > module load amber14 > > > module load intel-cluster-studio-2013-sp1 > > cd /home/ashoks/5_garima/pm/pm > mpirun -np 256 sander.MPI -O -i Prod.in -o Prod.out -p cd_cdpm7.prmtop -c > Hat.rst -r prod.rst -x prod.mdcrd -inf prod.info > > What is the problem i could not understand kindly provide your valuable > suggestion to overcome this issue? > > > > *Thank You and Best Wishes* > -- > *Regards* > Garima Singh > AcSIR-PhD Fellow > Biotechnology Division > C/o Dr. Ashok Sharma (Chief Scientist and Head Biotechnology Division) > Central Institute Of Medicinal And Aromatic Plant > CSIR-CIMAP > Lucknow > garimabioinfo.gmail.com > > > > > *INDIA* Please don't print this e-mail unless you really need to. Be Green > ! > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > > ------------------------------ > > Message: 8 > Date: Thu, 22 Jun 2017 08:17:46 -0400 > From: David A Case <david.case.rutgers.edu> > Subject: Re: [AMBER] Amber md in HPC : Job terminated > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: <20170622121746.3eufajajkasggdij.scarletmail.rutgers.edu> > Content-Type: text/plain; charset=us-ascii > > On Thu, Jun 22, 2017, Garima Singh wrote: > > > mpirun -np 256 sander.MPI -O -i Prod.in -o Prod.out -p cd_cdpm7.prmtop -c > > Hat.rst -r prod.rst -x prod.mdcrd -inf prod.info > > ...oooh... there are very few situations where sander.MPI will scale to 256 > threads. Consider running with many fewer nodes, which will ease the > problem > of having to have nearly the same number of atoms in all threads. I'm > guessing that you will find using so many threads slows down the > simulation. > (Apologies if you are running one of the exceptions, such as a very large > GB simulation...) In any event, using fewer nodes may be required to avoid > the problems you are seeing. > > Of course, check your simulation volume and visualize your trajectory to > make > sure that you don't have problems like vacuum bubbles etc. > > ....dac > > > > > ------------------------------ > > Message: 9 > Date: Thu, 22 Jun 2017 15:51:00 +0200 > From: SHAILESH KUMAR <shaile27_sit.jnu.ac.in> > Subject: [AMBER] Problem Imaging atoms of system crossing the PBC box > from opposite faces of box at the same time > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAF6Pu6W8FpV=68D1XSP-71ritWRbD3XB-s=p_e03_ > QDRJ49UgQ.mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Fellows, > > I have performed a MD simulation with coordinates wrapping enabled. Now I > am facing discontinuous trajectory problem. I tried to unwrap coordinates > and reimage but it did not helped. Investigating about the cause of problem > I found following things. > > 1. PBC Box dimensions: {88.588371 75.344688 67.300514 90.000000 90.000000 > 90.000000} > 2. Protein dimension (distance between coordinates of extreme points in > protein) as > {63.625731468200684 49.82566452026367 40.63145446777344} > > Unwrapping and Imaging was done as below with cpptraj. > > parm com.wat.leap.prmtop > trajin rst2_out.dcd 1 51000 10 > reference ../../../../02.leap/com/com.wat.leap.inpcrd > unwrap byres reference !:1-287 > center :123.HE2 mass origin reference > image origin center familiar com :123.HE2 byres !:1-287 > unwrap byatom reference :1-287 > center :123.HE2 mass origin reference > image origin center familiar com :123.HE2 byatom :1-287 > trajout com.strip_cr14.nc > go > > Atom :123.HE2 was nearest protein atom to the center of PBC box in initial > coordinates, hence it was chosen for centering protein to the box. > > Now, problem is that molecule has rotated during the simulation in the box > and hence atoms are crossing two opposite sides of the box at the same > time. So, when it is wrapped these atoms are appearing from opposite of > actual side it should be, leading to stretches of structure connected by > bonds length of box-dimension. > > So, I tried to construct a cubic box of side length 20 with is center at > the center of PBC-box. > as follows. > > Let centre of PBC-box has coordinates {cx cy cz} > then six-set of residues corresponding to residues beyond inner-cubic-box > faces were selected as > > set rset1 [atomselect top "protein and x < cx - 10"] > set rset1 [atomselect top "protein and x > cx + 10"] > set rset1 [atomselect top "protein and y < cy - 10"] > set rset1 [atomselect top "protein and y > cy + 10"] > set rset1 [atomselect top "protein and z < cz - 10"] > set rset1 [atomselect top "protein and z > cz + 10"] > > Now residues in these sets were unwraped > centering was done with atom closet to the center of corresponding face of > inner-cubic-box > and image was done for these set of residues. but it dis not work > > Other suggested options were also tried e.g. > > unwrap > autoimage > > with bymol, byres and byatom options with solute mask, all system mask, but > yet to succeed. > > Any help and suggestions in regard will be greatly appreciated. > > Thank you. > > Image of system with/without box waters shown is attached. If required, I > can share, prmtop and dcd files with some frames. > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: vmdscene2.pdf > Type: application/pdf > Size: 222716 bytes > Desc: not available > Url : http://lists.ambermd.org/mailman/private/amber/ > attachments/20170622/fc5cc3fb/attachment-0001.pdf > > ------------------------------ > > Message: 10 > Date: Thu, 22 Jun 2017 11:55:07 -0400 > From: Daniel Roe <daniel.r.roe.gmail.com> > Subject: Re: [AMBER] Problem Imaging atoms of system crossing the PBC > box from opposite faces of box at the same time > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAAC0qOYNAzitszRWBEf7h5y0ASguOn3JnOikAP2DgdLLcO5-RQ.mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > What happens if you just 'autoimage' (don't unwrap first)? > > -Dan > > On Thu, Jun 22, 2017 at 9:51 AM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in> > wrote: > > Dear Fellows, > > > > I have performed a MD simulation with coordinates wrapping enabled. Now I > > am facing discontinuous trajectory problem. I tried to unwrap coordinates > > and reimage but it did not helped. Investigating about the cause of > problem > > I found following things. > > > > 1. PBC Box dimensions: {88.588371 75.344688 67.300514 90.000000 90.000000 > > 90.000000} > > 2. Protein dimension (distance between coordinates of extreme points in > > protein) as > > {63.625731468200684 49.82566452026367 40.63145446777344} > > > > Unwrapping and Imaging was done as below with cpptraj. > > > > parm com.wat.leap.prmtop > > trajin rst2_out.dcd 1 51000 10 > > reference ../../../../02.leap/com/com.wat.leap.inpcrd > > unwrap byres reference !:1-287 > > center :123.HE2 mass origin reference > > image origin center familiar com :123.HE2 byres !:1-287 > > unwrap byatom reference :1-287 > > center :123.HE2 mass origin reference > > image origin center familiar com :123.HE2 byatom :1-287 > > trajout com.strip_cr14.nc > > go > > > > Atom :123.HE2 was nearest protein atom to the center of PBC box in > initial > > coordinates, hence it was chosen for centering protein to the box. > > > > Now, problem is that molecule has rotated during the simulation in the > box > > and hence atoms are crossing two opposite sides of the box at the same > > time. So, when it is wrapped these atoms are appearing from opposite of > > actual side it should be, leading to stretches of structure connected by > > bonds length of box-dimension. > > > > So, I tried to construct a cubic box of side length 20 with is center at > > the center of PBC-box. > > as follows. > > > > Let centre of PBC-box has coordinates {cx cy cz} > > then six-set of residues corresponding to residues beyond inner-cubic-box > > faces were selected as > > > > set rset1 [atomselect top "protein and x < cx - 10"] > > set rset1 [atomselect top "protein and x > cx + 10"] > > set rset1 [atomselect top "protein and y < cy - 10"] > > set rset1 [atomselect top "protein and y > cy + 10"] > > set rset1 [atomselect top "protein and z < cz - 10"] > > set rset1 [atomselect top "protein and z > cz + 10"] > > > > Now residues in these sets were unwraped > > centering was done with atom closet to the center of corresponding face > of > > inner-cubic-box > > and image was done for these set of residues. but it dis not work > > > > Other suggested options were also tried e.g. > > > > unwrap > > autoimage > > > > with bymol, byres and byatom options with solute mask, all system mask, > but > > yet to succeed. > > > > Any help and suggestions in regard will be greatly appreciated. > > > > Thank you. > > > > Image of system with/without box waters shown is attached. If required, I > > can share, prmtop and dcd files with some frames. > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > -- > ------------------------- > Daniel R. Roe > Laboratory of Computational Biology > National Institutes of Health, NHLBI > 5635 Fishers Ln, Rm T900 > Rockville MD, 20852 > https://www.lobos.nih.gov/lcb > > > > ------------------------------ > > Message: 11 > Date: Thu, 22 Jun 2017 18:47:41 +0200 > From: SHAILESH KUMAR <shaile27_sit.jnu.ac.in> > Subject: Re: [AMBER] Problem Imaging atoms of system crossing the PBC > box from opposite faces of box at the same time > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAF6Pu6UGo9BZWyv5m7mGU2HB0RbnY7VrJVr=5sS0Da=M1z01Sg.mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > I tried autoimage first as it is suggested in manual, but it did not > worked. Only after that I tried unwrap & image combination > > On Jun 22, 2017 5:57 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote: > > > What happens if you just 'autoimage' (don't unwrap first)? > > > > -Dan > > > > On Thu, Jun 22, 2017 at 9:51 AM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in> > > wrote: > > > Dear Fellows, > > > > > > I have performed a MD simulation with coordinates wrapping enabled. > Now I > > > am facing discontinuous trajectory problem. I tried to unwrap > coordinates > > > and reimage but it did not helped. Investigating about the cause of > > problem > > > I found following things. > > > > > > 1. PBC Box dimensions: {88.588371 75.344688 67.300514 90.000000 > 90.000000 > > > 90.000000} > > > 2. Protein dimension (distance between coordinates of extreme points in > > > protein) as > > > {63.625731468200684 49.82566452026367 40.63145446777344} > > > > > > Unwrapping and Imaging was done as below with cpptraj. > > > > > > parm com.wat.leap.prmtop > > > trajin rst2_out.dcd 1 51000 10 > > > reference ../../../../02.leap/com/com.wat.leap.inpcrd > > > unwrap byres reference !:1-287 > > > center :123.HE2 mass origin reference > > > image origin center familiar com :123.HE2 byres !:1-287 > > > unwrap byatom reference :1-287 > > > center :123.HE2 mass origin reference > > > image origin center familiar com :123.HE2 byatom :1-287 > > > trajout com.strip_cr14.nc > > > go > > > > > > Atom :123.HE2 was nearest protein atom to the center of PBC box in > > initial > > > coordinates, hence it was chosen for centering protein to the box. > > > > > > Now, problem is that molecule has rotated during the simulation in the > > box > > > and hence atoms are crossing two opposite sides of the box at the same > > > time. So, when it is wrapped these atoms are appearing from opposite of > > > actual side it should be, leading to stretches of structure connected > by > > > bonds length of box-dimension. > > > > > > So, I tried to construct a cubic box of side length 20 with is center > at > > > the center of PBC-box. > > > as follows. > > > > > > Let centre of PBC-box has coordinates {cx cy cz} > > > then six-set of residues corresponding to residues beyond > inner-cubic-box > > > faces were selected as > > > > > > set rset1 [atomselect top "protein and x < cx - 10"] > > > set rset1 [atomselect top "protein and x > cx + 10"] > > > set rset1 [atomselect top "protein and y < cy - 10"] > > > set rset1 [atomselect top "protein and y > cy + 10"] > > > set rset1 [atomselect top "protein and z < cz - 10"] > > > set rset1 [atomselect top "protein and z > cz + 10"] > > > > > > Now residues in these sets were unwraped > > > centering was done with atom closet to the center of corresponding face > > of > > > inner-cubic-box > > > and image was done for these set of residues. but it dis not work > > > > > > Other suggested options were also tried e.g. > > > > > > unwrap > > > autoimage > > > > > > with bymol, byres and byatom options with solute mask, all system mask, > > but > > > yet to succeed. > > > > > > Any help and suggestions in regard will be greatly appreciated. > > > > > > Thank you. > > > > > > Image of system with/without box waters shown is attached. If > required, I > > > can share, prmtop and dcd files with some frames. > > > > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > > > > -- > > ------------------------- > > Daniel R. Roe > > Laboratory of Computational Biology > > National Institutes of Health, NHLBI > > 5635 Fishers Ln, Rm T900 > > Rockville MD, 20852 > > https://www.lobos.nih.gov/lcb > > > > _______________________________________________ > > 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 > > > End of AMBER Digest, Vol 1973, Issue 1 > ************************************** > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Jun 29 2017 - 05:00:03 PDT