[gmx-users] Distance Restranints

Reza Esmaeili goldeagle.93 at gmail.com
Thu Feb 9 07:15:06 CET 2017

I’ve been trying to apply a distance restraint on a metal and 4 other coordinating atoms.

So I made 5 indices (each for one of the ligating atom and the metal) and then made 4 distance restraint .itp files with gmx genrestr.
gmx genrestr -f gro -n mdx -o itp -disre -disre_dist 0.1
So the pair must be restrained and allowed to move within 0.2 angstroms from their initial distance from the other peer.

Then I included the 4 tip files in the topology.
A 2ns production run shows the movement of the pairs is not limited to the distance mentioned in the tip files and is not within the 0.2 Angstroms.

Any ideas how to make this work and keep the atoms at the desired distance?!

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