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.abra...@gmail.com>
To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@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_arasteh2...@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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========================================
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
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