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

[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



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