[gmx-users] Position restraining of ions.

anu chandra anu80125 at gmail.com
Wed Jul 15 17:54:01 CEST 2015

Dear Gromcacs users,

I have carried out 25 ns simulation of membrane-protein systems. Now, I
would like to do position restrain of ions for the next 1-2 ns. I have KCl
in my system. I used ' genrestr ' for generating the position restrain for
ions  using the following command -

genrestr -f md50.gro -o ions-rest.itp

I have included ions-rest.itp in the .top file  with proper ' ifdef '  term
as mention in tutorials. Unfortunately, the grommp shows error message -  "
Atom index (2) in position_restraints out of bounds (1-1). This probably
means that you have inserted topology section "position_restraints"
in a part belonging to a different molecule than you intended to" . I have
seen from Gromcas mail list that many faced similar issues and this usually
comes from the mismatch in atom indices. Unfortunately, I could not find
complete solution for it yet. Few queries in this regard are,

1. How can I generate a position restrain file for ions or any set of
molecules in the system? my topology file have following hierarchy,

;       This is a standalone topology file
;       Created by:
;       GROMACS:      gmx pdb2gmx, VERSION 5.0.4
;       Executable:   /usr/local/gromacs/bin/gmx
;       Library dir:  /usr/local/gromacs/share/gromacs/top
;       Command line:
;         gmx pdb2gmx -f step5_IP3R.pdb -ter
;       Force field was read from the standard Gromacs share directory.

; Include forcefield parameters
#include "charmm36-jun2015.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein.itp"
#include "topol_Protein2.itp"
#include "topol_Protein3.itp"
#include "topol_Protein4.itp"
#include "POPC.itp"

; Include water topology
#include "charmm36-jun2015.ff/tip3p.itp"

; Include topology for ions
#include "charmm36-jun2015.ff/ions.itp"

[ system ]
; Name

[ molecules ]
; Compound        #mols
Protein             1
Protein2            1
Protein3            1
Protein4            1
POPC              295
POT                 85
CL                   122
SOL                24892

2. Where all I can use the .itp file for a particular group generate with '
genrestr' command?

Many thanks in advance


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