[gmx-users] atom freezing during simulation

[Justin Lemkul]

On 5/3/15 1:17 AM, mah maz 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?
>

Either your frozen groups are set up incorrectly or you're looking at the wrong 
atoms.  What does gmx traj report about the coordinates of the atoms in those 
groups?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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