[gmx-users] Re: inflate gro

Sweta Iyer iyer at wehi.EDU.AU
Thu Jul 21 05:28:02 CEST 2011

Hi Justin,

Thanx for the suggestion. This is how my topology looks like with the
strong position restraint included for the protein:

; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp"

; Include chain topologies
#include "complex6_Protein_chain_X.itp"
#include "complex6_Protein_chain_Y.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"

#include "strong_posre.itp"

; Include chain topology for DMPC
#include "dmpc.itp"

; Include water topology
#include "gromos53a6.ff/spc.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; Include topology for ions
#include "gromos53a6.ff/ions.itp"

[ system ]
; Name

[ molecules ]
; Compound        #mols
Protein_chain_X     1
Protein_chain_Y     1
DMPC		    125

I think the tutorial asks to include a section in the topology similar to

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