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

[David]

-------- 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.
________________________________________________________________________
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
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