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
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