[gmx-users] Graphene topology file

[Justin Lemkul]

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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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