[gmx-users] Position restraints

davhak davhak at gmail.com
Mon Feb 24 10:23:36 CET 2014

Dear All,

I try to restrain the movement of a certain particle in all cholesterol 
molecules (coarse-grained model) in Z direction. To do this I add a [
position_restraints ] section under the [ moleculetype ] of cholesterol itp
file like:

  CHOL 		1

[ position_restraints ]
;  i funct       fcx        fcy        fcz
8    1          0          0       100000

The problem is that during the simulation the restrained atoms already after
a few hundred ns move by ~0.2 nm in average.  No matter whether the
restraining force constant is set to 100000 0r 1000. The log file shows that
the restraining energy varies around 300-500 kJ/mol regardless of the
restraining force constant value (there are over 200 cholesterol molecules
in the system).

As expected one gets the same outcome when the position restraint is applied
according to the Gromacs manual i.e. by setting a define in the mdp file and
including a separate position_restraints] itp file within an #ifdef #endif
clause right after the inclusion of the cholesterol itp file.

It should be something trivial missing in my understanding of how position
restraint should be applied. 

Thanks very much for any suggestion.

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