[gmx-users] Position restraining of ions.

[Justin Lemkul]

On 7/15/15 11:53 AM, anu chandra wrote:
> 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
> Titile
>
> [ 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?
>

Restraints are applied on a per-moleculetype basis; hence genrestr is very 
limited in what it can do (multiple molecules won't work without considerable 
effort).

The only way to restrain the ions within this setup is to modify ions.itp to 
specify restraints within the relevant [moleculetype] directives.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================