[gmx-users] [Fwd: Position restraints in GROMACS]

David spoel at xray.bmc.uu.se
Sun Aug 14 09:20:25 CEST 2005

-------- Forwarded Message --------
From: Bob Johnson <robertjo at physics.upenn.edu>
To: spoel at xray.bmc.uu.se
Subject: Position restraints in GROMACS
Date: Sat, 13 Aug 2005 16:11:38 -0400
Hello Dr. Spoel,
First off, I wanted to thank you for all your responses to my questions on the
GROMACS mailing list. Secondly, I had a question about position restraints in
GROMACS. You mentioned that I had to download the CVS version of GROMACS in
order to use them. I downloaded it but am having problems installing it. Is the
CVS version really needed? Another person in my group believed that she used
them on the normal version of GROMACS. I am placing the include posre.itp
statement at the end of the topology file. I want to restrain atoms 1-2080 so I
placed the following statement:
[ position_restraints ]
;atom   type     fx     fy    fz
1        1       1e9   1e9    1e9
2        1       1e9   1e9    1e9
and so on

I am getting the following error message by grompp:

WARNING 1 [file "posre.itp", line 5]:
  No default Position Rest. types for perturbed atoms, using normal values

and similarly for line 6-10. Would the CVS version alleviate these issues?
Thanks for your time,
Bob Johnson
University of Pennsylvania
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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 mailing list