[gmx-users] Position restraining of ions.

[Gordan Horvat]

You can copy the part regarding the certain ion type from ions.itp to a 
separate itp file and #include that itp file into a top file. Then 
#include the position restraint file that has restraints for only one 
ion of that type at the end of that new itp file. By this manner you can 
even split a group of same ions (for example, some potassium ions are 
restrained and others are not) by making separate itp files for 
potassium ions in which you specify different [ moleculetype ] names for 
each file and doing that accordingly at the [ molecules ] table at the 
end of a top file. Of course, when you split groups you need to know the 
positions of ions of interest in a system structural file (gro or pdb), 
as they need to be listed in the same order in the [ molecules ] table.

Gordan

On 7/16/2015 2:36 AM, Justin Lemkul wrote:
>
>
> 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
>