[gmx-users] 答复: position restraint during NVT equllibration

sunyeping sunyeping at aliyun.com
Wed Feb 19 15:08:14 CET 2014

发件人:Justin Lemkul <jalemkul at vt.edu>
发送时间:2014年2月19日(星期三) 21:35
收件人:gromacs <gmx-users at gromacs.org>; 孙业平 <sunyeping at aliyun.com>
主 题:Re: [gmx-users] position restraint during NVT equllibration

On 2/19/14, 4:20 AM, sunyeping wrote:
> Dear all,I am doing MD simulation on a protien which has three chains. It needs position restrain when doing NVT equillibration. When do MD simulation on a protein having only one chains, pdb2gmx will generation a  posre.itp file. By including
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> in topol.top file and including
> define		= -DPOSRES
> in the NVT.mdp file
> the position restrain on potein can be realized. However, if the protein has three chains, pdb2gmx generates not a  posre.itp file but three itp files ( posre_Protein_chain_A.itp, posre_Protein_chain_B.itp, posre_Protein_chain_C.itp). Under such circumstance, how should we do position restaint on potein?

Have you looked at the topology?  You'll find a strikingly similar control 
structure for each of the chains.



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

==================================================tThe topology is as following:;;	File 'topol.top' was generated;	By user: root (0);	On host: localhost.localdomain;	At date: Wed Feb 19 09:58:58 2014;;	This is a standalone topology file;;	It was generated using program:;	pdb2gmx - VERSION 5.0-dev;;	Command line was:;	pdb2gmx -f KI-10_JKL.pdb -ignh -o complex.gro;;	Force field was read from the standard Gromacs share directory.;
; Include forcefield parameters#include "gromos43a1.ff/forcefield.itp"
; Include chain topologies#include "topol_Protein_chain_J.itp"#include "topol_Protein_chain_K.itp"#include "topol_Protein_chain_L.itp"
; Include water topology#include "gromos43a1.ff/spce.itp"
#ifdef POSRES_WATER; Position restraint for each water oxygen[ position_restraints ];  i funct       fcx        fcy        fcz   1    1       1000       1000       1000#endif
; Include topology for ions#include "gromos43a1.ff/ions.itp"
[ system ]; NameProtein in water
[ molecules ]; Compound        #molsProtein_chain_J     1Protein_chain_K     1Protein_chain_L     1SOL         19193NA               64CL               58
 What do you mean when you talking about "strikingly similar control structure for each of the chains"? 

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