[gmx-users] Graphene topology file
SUKRITI002 at e.ntu.edu.sg
Mon Aug 4 17:10:55 CEST 2014
Hi gromacs users,
I was able to simulate graphene sheet in water. Now I want to simulate functionalised graphene sheet with -OH groups attached randomly to graphene sheet. I modified atomname2type.n2t file by adding oxygen and hydrogen groups to it. Following is my .n2t file:
C opls_995 0 12.011 2 C 0.142 C 0.142
C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142
C opls_997 0 12.011 1 C 0.142
C opls_998 0 12.011 4 C 0.142 C 0.142 C 0.142 O 0.143
OH opls_154 -0.7 15.9994 2 C 0.143 HO 0.96
HO opls_155 0.435 1.008 1 OH 0.96
But when I give following x2top command, I get error message :
g_x2top -f grap1.pdb -o graphene.top -name GRA -nexcl 3 -pbc
Could only find a forcefield type for 256 out of 456 atoms
Can anyone please let me know what can be creating the problem?
Thanks and Regards
Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
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 17, 2014 7:50 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Graphene topology file
On 7/17/14, 7:16 AM, #SUKRITI GUPTA# wrote:
> Hi gromacs users,
> I read that for slab geometries where you need pbc in xy, you can use pbc=xyz and have a slab of vacuum
> in between the periodic images in z and use ewald3dc (Yeh and Berkowitz method). So I changed my mdp file extended my box in z direction( with no solvent molecules) and did the energy minimization and npt again. In em, the box looks fine but with npt again I get same output i.e. water molecules fly away and box size in z direction increases drastically, through the vacuum layer is still maintained. Then I changed my pressure coupling to Parinello- Rahman instead of Berendsen. This time npt runs some steps and gives an error message:
> Fatal error:
> One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.
> Can anyone please let me know how can I solve this problem. If we have a layer of vacuum, wont the box size reduce in npt and cause this error? Should I skip npt and directly do nvt?
If you need to maintain a vacuum layer, your box needs to be incompressible
along that direction, i.e. use semiisotropic coupling and set compressibility =
0 in the .mdp file for the z-direction.
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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