[gmx-users] freezegrps is not working

trinidad.mendez at usc.es trinidad.mendez at usc.es
Wed Dec 9 16:28:51 CET 2015

Dear all,

I'm trying to perform an energy minimization in which several atoms  
must have fixed positions. For that purpose I'm using an steepest  
descent algorithm and I'm including in the *.mdp file the lines  
concerning freezegrps, freezedim (the 3 dimensions) and energygrp-excl.

However, the atoms expected to be frozen have different positions  
after the energy minimization. Not all of them are moved, but a few of  
them have a different X coordinate, other atoms get a different Y  
coordinate and so on...

I've also tried to fix these atoms by using [position_restraints] in  
the corresponding [moleculetype] of the topology file with a force  
constant of 10000 in each dimension, but in this case I'm not able to  
freeze any atom (the three coordinates are changed for all of them).

The group of atoms that I want to fix is included in the index.ndx  
file and the version I'm using is the 5.0.2 one.

Thanks in advance!

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