[gmx-users] Restrained Molecule is Moving

Jennifer Casey 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:

#ifdef POSRES
#include "posre_Na+.itp"

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
file afterwards.

I really appreciate the help.

Thank you,
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