[gmx-users] simulation of molecules in solid state

[Justin Lemkul]

On 4/17/17 3:32 PM, Saumyak Mukherjee wrote:
> Dear Users,
>
> I have a .cif (Crystallography Information File) of a crystal of charged
> molecules along with counter ions. I want to simulate it to study its
> stability at room temperature. Is this possible in GROMACS. If so, how is
> it done?
>

Like anything else - build a topology for the components, specify how many of 
each are in the system in the .top, and away you go.  You may have to use 
external tools/programs to build the topology/parametrize the species of interest.

-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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