[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"
#endif
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif
; Include chain topology for DMPC
#include "dmpc.itp"
; Include water topology
#include "gromos53a6.ff/spc.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 "gromos53a6.ff/ions.itp"
[ system ]
; Name
Protein
[ 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
this?!
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