[gmx-users] atom freezing during simulation

[Justin Lemkul]

On 5/4/15 1:10 AM, mah maz wrote:
> 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?

No.  Valid options are "Y" (yes) or "N" (no) for each dimension.  See 
http://manual.gromacs.org/online/mdp_opt.html#neq

In your case, you're freezing along the y-axis only.

-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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