[gmx-users] Position restraining of ions.
Gordan Horvat
ghorvat at chem.pmf.hr
Thu Jul 16 12:32:45 CEST 2015
#ifdef REST_ON
#include "POT_rest.itp"
#endif
should go at the end of POT_rest.itp file and
#ifdef REST_ON
#include "CL_rest.itp"
#endif
should go at the end of CL.itp file. The restraint you listed restraints
the first atom of every molecule of the type stated in the corresponding
itp file. Since potassium and chloride ions are monoatomic, that should
work fine.
Elsewise, you can just put the line
#include "ionX_rest.itp"
at the end of the ionX.itp file which will turn on restraints
automatically without having to define -DPOSIONX keyword in mdp file.
Gordan
On 7/16/2015 11:51 AM, anu chandra wrote:
> 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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