[gmx-users] water position restraints

[Shima Arasteh]

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?





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 
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