[gmx-users] water position restraints

[Justin Lemkul]

On 6/2/13 7:57 AM, Shima Arasteh wrote:
> I just applied genrestr command:
> #genrestr -f minim.gro -o water_posre.itp -fc 100000 100000 100000
> And then I just chose the water to create the water_posre.itp.
> Would not that work?
>

No, it won't.  You can't run genrestr on a configuration with multiple 
molecules.  Position restraints are applied based on moleculetype-specific 
numbering, not atom numbering in a coordinate file; thus genrestr only works if 
using a single molecule in the input (note that the help text tells you this).

The approach outlined before is redundant and will cause a fatal error due to 
atom numbering.  If you want to restrain water molecules, the default #ifdef 
that is already built into the topology does all the work for you.  You don't 
need to do anything.  If, for some reason, you feel a stronger force constant is 
required, just change it using a text editor.

-Justin

>
>
>
>
> Sincerely,
> Shima
>
>
> ________________________________
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Sunday, June 2, 2013 3:35 PM
> Subject: Re: [gmx-users] water position restraints
>
>
>
> What's in that .itp? You can only restrain all the waters that have that moleculetype. See http://www.gromacs.org/Documentation/How-tos/Position_Restraints
>
>
>
> On Sun, Jun 2, 2013 at 9:52 AM, Shima Arasteh <shima_arasteh2001 at yahoo.com> wrote:
>
> Dear GMX users,
>>
>> I' d like to put the position restraints on water oxygen atoms.
>> To do so, I made a water_posre.itp file. Then I modified the top file, as this, but didn't work:
>>
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct       fcx        fcy        fcz
>>     1    1       1000       1000       1000
>> #include "water_posre.itp"
>> #endif
>>
>>
>> Would you please help me here? I don't know how I change the fcx, fcy, and fcz. Is it possible to change the fc values 1000 to 100000 in top file by just text editing as below:
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct       fcx        fcy        fcz
>>     1    1       100000       100000       100000
>> #include "water_posre.itp"
>> #endif
>>
>>
>>
>>
>>
>>
>> Sincerely,
>> Shima
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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