Re: [gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher
On Thu, Aug 1, 2013 at 10:10 PM, akk5r wrote: > Hi All, > > I am trying to run a membrane protein simulation on Gromacs 4.6 using the > Charmm 36 force field parameters. > > I found the following parameters on the gromacs mailing list for Charmm 36: > *; nblist cut-off > rlist= 1.2 > ; long-range cut-off for switched potentials > rlistlong= 1.4 > > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = PME > rcoulomb-switch = 0 > rcoulomb = 1.2 > ; Relative dielectric constant for the medium and the reaction field > epsilon_r= 1 > epsilon_rf = 1 > ; Method for doing Van der Waals > vdw-type = switch > ; cut-off lengths > rvdw-switch = 0.8 > rvdw = 1.2 > ; Apply long range dispersion corrections for Energy and Pressure > DispCorr = No * > > > > > Putting these setting into my .mdp file, I then get this error on grompp: > > *ERROR 1 [file nvt.mdp]: > With Verlet lists only cut-off LJ interactions are supported* > > I then turned off the Verlet cut-off scheme and was able to create a .tpr > file. That's up to you, of course. Your other option is to use Verlet and a plain cut-off at 1.2nm; over the distance from 0.8 and 1.2, the difference between plain cutoff and force-shifted VDW is probably irrelevant anyway. > Then I ran my .tpr on mdrun and got the following error: > > *Program mdrun, VERSION 4.6.1 > Source code file: /home/akk5r/Downloads/gromacs-4.6.1/src/kernel/runner.c, > line: 824 > > Fatal error: > OpenMP threads have been requested with cut-off scheme Group, but these are > only supported with cut-off scheme Verlet > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors* > > At this point, I don't know what to do. I have to run this job on a cluster > system due to the size of the system. Sure, but your commands to your cluster are setting up the environment with OMP_NUMTHREADS>1. With the group scheme, you want one MPI rank per core. Mark > Does any one know how to run Charmm 36 > simulations on Gromacs 4.6 or higher using Verlet cut-off scheme? > > Best Wishes, > Ali > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Using-Charmm-36-forcefield-on-Gromacs-4-6-or-higher-tp5010290.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher
On 8/1/13 4:10 PM, akk5r wrote: Hi All, I am trying to run a membrane protein simulation on Gromacs 4.6 using the Charmm 36 force field parameters. I found the following parameters on the gromacs mailing list for Charmm 36: *; nblist cut-off rlist= 1.2 ; long-range cut-off for switched potentials rlistlong= 1.4 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.2 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 0.8 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No * Putting these setting into my .mdp file, I then get this error on grompp: *ERROR 1 [file nvt.mdp]: With Verlet lists only cut-off LJ interactions are supported* I then turned off the Verlet cut-off scheme and was able to create a .tpr file. Then I ran my .tpr on mdrun and got the following error: *Program mdrun, VERSION 4.6.1 Source code file: /home/akk5r/Downloads/gromacs-4.6.1/src/kernel/runner.c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors* At this point, I don't know what to do. I have to run this job on a cluster system due to the size of the system. Does any one know how to run Charmm 36 simulations on Gromacs 4.6 or higher using Verlet cut-off scheme? The error messages are inconsistent. Can you please post a full .mdp file and your exact mdrun command? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher
Hi, just try to disable OpenMP threads, unsetting OMP_NUM_THREADS environment variable Francesco 2013/8/1 akk5r > Hi All, > > I am trying to run a membrane protein simulation on Gromacs 4.6 using the > Charmm 36 force field parameters. > > I found the following parameters on the gromacs mailing list for Charmm 36: > *; nblist cut-off > rlist= 1.2 > ; long-range cut-off for switched potentials > rlistlong= 1.4 > > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = PME > rcoulomb-switch = 0 > rcoulomb = 1.2 > ; Relative dielectric constant for the medium and the reaction field > epsilon_r= 1 > epsilon_rf = 1 > ; Method for doing Van der Waals > vdw-type = switch > ; cut-off lengths > rvdw-switch = 0.8 > rvdw = 1.2 > ; Apply long range dispersion corrections for Energy and Pressure > DispCorr = No * > > > > > Putting these setting into my .mdp file, I then get this error on grompp: > > *ERROR 1 [file nvt.mdp]: > With Verlet lists only cut-off LJ interactions are supported* > > I then turned off the Verlet cut-off scheme and was able to create a .tpr > file. > > Then I ran my .tpr on mdrun and got the following error: > > *Program mdrun, VERSION 4.6.1 > Source code file: /home/akk5r/Downloads/gromacs-4.6.1/src/kernel/runner.c, > line: 824 > > Fatal error: > OpenMP threads have been requested with cut-off scheme Group, but these are > only supported with cut-off scheme Verlet > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors* > > At this point, I don't know what to do. I have to run this job on a cluster > system due to the size of the system. Does any one know how to run Charmm > 36 > simulations on Gromacs 4.6 or higher using Verlet cut-off scheme? > > Best Wishes, > Ali > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Using-Charmm-36-forcefield-on-Gromacs-4-6-or-higher-tp5010290.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Oteri Francesco, PhD https://sites.google.com/site/francescooteri -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher
Hi All, I am trying to run a membrane protein simulation on Gromacs 4.6 using the Charmm 36 force field parameters. I found the following parameters on the gromacs mailing list for Charmm 36: *; nblist cut-off rlist= 1.2 ; long-range cut-off for switched potentials rlistlong= 1.4 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.2 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 0.8 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No * Putting these setting into my .mdp file, I then get this error on grompp: *ERROR 1 [file nvt.mdp]: With Verlet lists only cut-off LJ interactions are supported* I then turned off the Verlet cut-off scheme and was able to create a .tpr file. Then I ran my .tpr on mdrun and got the following error: *Program mdrun, VERSION 4.6.1 Source code file: /home/akk5r/Downloads/gromacs-4.6.1/src/kernel/runner.c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors* At this point, I don't know what to do. I have to run this job on a cluster system due to the size of the system. Does any one know how to run Charmm 36 simulations on Gromacs 4.6 or higher using Verlet cut-off scheme? Best Wishes, Ali -- View this message in context: http://gromacs.5086.x6.nabble.com/Using-Charmm-36-forcefield-on-Gromacs-4-6-or-higher-tp5010290.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
