[gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher

[Mark Abraham]

On Thu, Aug 1, 2013 at 10:10 PM, akk5r <akk5r at virginia.edu> 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.
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