[gmx-users] atom freezing during simulation

[mah maz]

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!
>