[gmx-users] freeze group

Mark Abraham mark.abraham at anu.edu.au
Tue Jan 9 13:38:58 CET 2007

> Hello wisdoms!
> We are performing the simulation of a protein of which the ion is
> surrounded by three aminoacids with in nearly 3A distance.
> Is it right to set my ion in the freeze group since it moves out of box
> during EM steps

> Else is there any strategy to fix the bug so that the coordinate bond
> can’t be affected during the simulation.

If I understand you correctly, you want the ion to stay within the
coordination sphere of the three amino acids. If so then you want to be
using distance restraints of some kind... probably a harmonic bond. See
table 5.4 and then look around chapters 4 and 5. You can even use LINCS to
constrain them to a specific length, once a bond exists.

By the way, speaking strictly you don't have a "bug", which would be a
problem with the structure of the gromacs code. You are having a problem
telling the simulation to do what you want it to do. Hard-working
developers can get annoyed when you use the word "bug", which ascribes to
them a fault that is almost assuredly your own :-)


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