[gmx-users] position restraint during NVT equllibration

Justin Lemkul jalemkul at vt.edu
Wed Feb 19 14:41:35 CET 2014

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


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