[gmx-users] Freeze a group of atoms in gromacs

[Justin Lemkul]

On 2/7/17 10:17 AM, ARNAB MUKHERJEE wrote:
> Hello,
>
> I am simulating a course grained DNA with counterions. I want to know if
> there is a way in gromacs to freeze all the degrees of freedom of DNA, so
> as to completely restrict its motion. So, the DNA in my system will be
> fixed while the ions will be moving. How can I achieve this in gromacs?
>

Freezing atoms can be done using the conveniently named freezegrps option:

http://manual.gromacs.org/documentation/2016.2/user-guide/mdp-options.html#non-equilibrium-md

-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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