[gmx-users] position restraints convention
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.
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
More information about the gromacs.org_gmx-users