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

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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