[gmx-users] position restraints convention

David spoel at xray.bmc.uu.se
Thu Feb 6 18:21:04 CET 2003

On Thu, 2003-02-06 at 18:08, Senthil Kandasamy wrote:
> From: Senthil Kandasamy <senthilk at engin.umich.edu>
> To: gmx_users at gromacs.org
> Cc: senthilk at umich.edu
> Subject: position restraints convention
> Date: 06 Feb 2003 12:06:21 -0500
> 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...
There is no right way... Wrong ways plenty of course. You can check
which atoms are restrained by using 
gmxdump -s topol.tpr | more

then search for POSRES

you will see the atom number. coordinates and force constants.

> Thanks.
> Senthil
Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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