[gmx-users] Restrained Molecule is Moving
jrcasey20 at gmail.com
Wed Feb 3 02:58:58 CET 2010
I am trying to restrain Na+ to a specific position (0.487, 1.620, 1.620) of
my box of dimensions 3.2418 X 3.2418 X 3.2418 nm. The box is also full of
253 THF molecules. I added the following to the bottom of my .itp file:
I wrote the posre_Na+.itp file myself, it just includes the position
restraints for Na+, which is atom 1 in my .gro file, and my posre_Na+.itp
file deals with atom 1. The force constants are all 1000.
Under the .mdp file, I also made sure that define = -DPOSRES.
I get no errors when things run, but I do get my Na+ moving around. After I
do energy minimization, Na+ ends up at the position (0.373, 1.504, 1.226).
I also do not notice anything about position restraints appearing in my .log
I really appreciate the help.
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