[gmx-users] position restraint during NVT equllibration

sunyeping sunyeping at aliyun.com
Wed Feb 19 10:27:36 CET 2014

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"

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?
Thanks in advance


Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences

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