[gmx-users] Problem with constant distance

[Justin Lemkul]

On 12/29/15 3:27 AM, Samith Rathnayake wrote:
> Dear All,
>
> I just want to run a molecular dynamics simulation in gromacs  with
> maintain a constant distance (like constrain the distance) between  two
> molecules in a specific period of time.(want to maintain the constant
> distance in the entire time period).
>
> ​Is there any way to simulate this kind of system?
>

http://manual.gromacs.org/documentation/5.1.1/user-guide/mdp-options.html#com-pulling

Use the "constraint" method to keep the distance fixed, or "umbrella" to 
restrain it via a harmonic biasing potential.

-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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