[gmx-users] Graphene topology file
jalemkul at vt.edu
Thu Jul 10 14:30:29 CEST 2014
On 7/10/14, 1:29 AM, #SUKRITI GUPTA# wrote:
> Hi Justin,
> I did simulation 2 times, once with PBC in xy with walls and other time with pbc in xyz.
> For pbc in xy with walls with following wall parameters:
> nwall = 2
> wall_type = 12-6
> wall_density = 5 5
> wall_atomtype = opls_995 opls_996
> wall_r_linpot = 1
> wall_ewald_zfac = 3
> Energy minimization runs fine but npt shows following errror and is terminated:
> Step 20:
> The charge group starting at atom 796 moved than the distance allowed by the domain decomposition in direction X
> distance out of cell -0.290927
> New coordinates: 2.411 2.006 0.982
> Old cell boundaries in direction X: 0.000 2.702
> New cell boundaries in direction X: 0.000 2.702
> Program mdrun, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 4124
> Fatal error:
> A charge group moved too far between two domain decomposition steps
> This usually means that your system is not well equilibrated
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> For pbc in xyz, both energy minimization and npt run but the water is suddenly moving far away from the graphene sheet any tries to agglomerate together causing the box size to increase drastically. It is almost like the box is about to explode. Its size changes from (2.70200 2.55300 4.00000) to (11.46117 10.82915 16.96695). The box expands in x,y and z all directions.
Without full .mdp files and some images demonstrating what's going on, it's too
hard to guess at what's happening here.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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