Re: [gmx-users] REMD - subsystems not compatible
Thanks Mark for reminding me about the existence of the log files. Problem solved, the difference is clearly indicated (number of atoms, my stupid mistake. Cheers /Per > 24 apr. 2019 kl. 16:51 skrev Mark Abraham : > > Hi, > > Generally the REMD code has written some analysis to the log file above > this error message that should provide context. > > More generally, you can use gmx check to compare the .tpr files and observe > that the differences between them are only what you expect. > > Mark > > On Wed, 24 Apr 2019 at 15:28, Per Larsson wrote: > >> Hi gmx-users, >> >> I am trying to start a replica exchange simulation of a model peptide in >> water, but can’t get it to run properly. >> I have limited experience with REMD, so I thought I’d ask here for all the >> rookie mistakes it is possible to do. >> I have also seen the earlier discussions about the error message, but >> those seemed to be related to restarts and/or continuations, rather than >> not being able to run at all. >> >> My gromacs version is 2016 (for compatibility reasons), and the exact >> error message I get is this: >> >> --- >> Program: gmx mdrun, version 2016.5 >> Source file: src/gromacs/mdlib/main.cpp (line 115) >> MPI rank:32 (out of 62) >> >> Fatal error: >> The 62 subsystems are not compatible >> >> I followed Marks tutorial on the gromacs website and have a small >> bash-script that loops over all desired temperatures, run equilibration >> etc. >> I then start the simulation like this: >> >> $MPIRUN $GMX mdrun $ntmpi -ntomp $ntomp -deffnm sim -replex 500 -multidir >> ~pfs/ferring/gnrh_aa/dipep_remd/sim* >> >> What could be the source of this incompatibility? >> >> Many thanks >> /Per >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD - subsystems not compatible
Hi gmx-users, I am trying to start a replica exchange simulation of a model peptide in water, but can’t get it to run properly. I have limited experience with REMD, so I thought I’d ask here for all the rookie mistakes it is possible to do. I have also seen the earlier discussions about the error message, but those seemed to be related to restarts and/or continuations, rather than not being able to run at all. My gromacs version is 2016 (for compatibility reasons), and the exact error message I get is this: --- Program: gmx mdrun, version 2016.5 Source file: src/gromacs/mdlib/main.cpp (line 115) MPI rank:32 (out of 62) Fatal error: The 62 subsystems are not compatible I followed Marks tutorial on the gromacs website and have a small bash-script that loops over all desired temperatures, run equilibration etc. I then start the simulation like this: $MPIRUN $GMX mdrun $ntmpi -ntomp $ntomp -deffnm sim -replex 500 -multidir ~pfs/ferring/gnrh_aa/dipep_remd/sim* What could be the source of this incompatibility? Many thanks /Per -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Non-symmetric PMF across lipid bilayer
Hi, Thanks Justin, but shouldn't the PMF be (more or less) symmetric anyway, given the inherent bilayer symmetry? In this case I have designed the two leaflets in the bilayer to have non-identical lipid composition, so then I think using -sym would obliterate any differences between the leaflets, no? On Wed, Nov 21, 2018 at 2:24 PM Justin Lemkul wrote: > > > On 11/21/18 7:22 AM, Gmx QA wrote: > > Hi all gmx-users > > > > I am working on calculating the PMF using umbrella sampling of a (rather > > large) molecule across a lipid bilayer. I have set up my umbrellas with a > > 0,2 nm spacing, and run each window for 100 ns. > > > > The problem is that the resulting PMF is not symmetric with respect to > the > > bilayer center. Initially is looks ok, but when the molecule is exiting > the > > bilayer on the other side again, the PMF does not go back to (roughly) > the > > same value as before entering the bilayer. > > > > I have uploaded the PMF file here: > > https://files.fm/u/7ec2rshc > > You didn't get a symmetric profile because you didn't ask for one. Use > the -sym option. > > -Justin > > > Any comments or suggestions are much appreciated. I understand the > problems > > and issues about calculations of a converged PMF with larger molecules, > but > > nevertheless I would have expected my PMF to be symmetric, albeit perhaps > > not converged. > > > > Thanks > > /PK > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
