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 list gmx-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
