[gmx-users] Position restraining of ions.

[anu chandra]

Hi,

Thanks for your prompt reply. I have modified the top file as shown below.
Though it looks working fine for me, can you please have quick look into it.

***********************************************************************************************************
r
;       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 "POT.itp"

#ifdef REST_ON
#include "POT_rest.itp"
#endif

#include "CL.itp"

#ifdef REST_ON
#include "CL_rest.itp"
#endif

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


[ system ]
; Name
Titile

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


And my POT_rest.itp and CL_rest have similar format as follows,


***************************************************************
; position restraints for POT of GROningen MAchine for Chemical Simulation

[ position_restraints ]
;  i funct       fcx        fcy        fcz
    1    1       1000       1000       1000

***********************************************************************

and I have ' define  = -DREST_ON ' in mdp file.


Hope what I am doing is right?


Many thanks
Anu


On Thu, Jul 16, 2015 at 7:32 AM, Gordan Horvat <ghorvat at chem.pmf.hr> wrote:

> 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
>>
>>
>
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