[gmx-users] Simulations enclosed in sphere and arbitrary defined non standard interactions

[Justin Lemkul]

On 4/5/16 9:29 AM, Michał Kadlof wrote:
> Hello,
>
> I would like to run my simulations inside closed sphere. It may be something like soft-walls potential (0 inside a sphere, and proportional to r^2 outside sphere with force directed to the center of sphere) or something similar. Is it possible with Gromacs? I'm not afraid to mess up with a Gromacs code a little bit if it necessary.
>

Flat-bottom position restraints will do this.

>
> I'm also curious if it possible to add harmonic interaction between arbitrary chosen two beads in simulations. I would also like to define different interaction constant for each such spring separately.
>

Use the pull code.  In version 5.1 there is the ability to define as many such 
interactions as you like.

-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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