[gmx-users] position restraints convention

[Anton Feenstra]

Senthil Kandasamy wrote:
> 
> 
> ------------------------------------------------------------------------
> 
> Subject:
> position restraints convention
> From:
> Senthil Kandasamy <senthilk at engin.umich.edu>
> Date:
> 06 Feb 2003 12:06:21 -0500
> To:
> gmx_users at gromacs.org
> 
> 
> What is the convention on where the position restraints are specified?
> E.g., in a  protein/lipid/water system, is it better to specify
> POSRE_PROTEIN in protein.itp and POSRE_LIPID in lipid.itp  in the
> respective molecule sections or is it better to specify both
> POSRE_PROTEIN and POSRE_LIPID in the topol.top file?
> 
> What do people prefer and is there a RIGHT way to do it?
> I have a system where part of the water, part of the protein and some of
> the lipids are constrained and am not sure if I am simulating what I
> intend to...

As David said, there are many right and even much more wrong ways... ;-)

I'd suggest the following. Since in Gromacs position restraints are part
of the molecule definition, it makes sense to include them in the actual
molecule .itp file. Otherwise, you always have to make sure to put the
things in exactly the right order in the .top file.

Additionally, in your .itp file you might want to change the line
#ifdef POSRE_PROTEIN
into
#if defined ( POSRE_PROTEIN || POSRE )
and similarly for POSRE_LIPID (and possibly POSRE_WATER), so they will
all also respond when you set -DPOSRE, and turn them all on.


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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