[gmx-users] Graphene topology file
SUKRITI002 at e.ntu.edu.sg
Thu Jul 10 07:29:52 CEST 2014
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:
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
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.
Thanks and Regards
Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459)
Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:erian.ntu.edu.sg
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Thursday, July 10, 2014 1:26 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Graphene topology file
On 7/9/14, 9:06 AM, #SUKRITI GUPTA# wrote:
> Thanks for the reply Justin. I just checked my box size again and found it to
> be smaller than the required. Hence I changed the size and ran the simulation
> again. This time energy minimization happened correctly without any change in
> the graphene structure. But when I am doing npt, 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 2.5A to 11A.
> Can you please help me figure out the problem.
Does the box expand along z? Are you using walls? If not, you should be, in
the case of pbc = xy.
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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