[gmx-users] atom freezing during simulation

mah maz mahmaz71 at gmail.com
Mon May 4 07:10:37 CEST 2015

Hi Justin,
Unfortunately, I am looking at the right atoms! Coordinates of the frozen
atoms are different from their initial ones and they have non-zero
velocities. I set up the .mdp file as follows:
freezegrps = frz1 frz2
freezdim = x y z  x y z
Is it the correct way of setting up frozen groups?
Thank you!

On Sun, May 3, 2015 at 9:47 AM, mah maz <mahmaz71 at gmail.com> wrote:

> Dear all,
> I need to freeze some atoms in my system not to move during simulation. I
> used freezegrps and freezdim options but after simulation, I can see that
> the fixed atoms also moved and their coordinates changed. What can I do to
> fix their positions? Should I couple them with thermostat and assign low
> temperatures to avoid their motion?
> Thanks!

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