[gmx-users] Problem with constant distance

Samith Rathnayake samithzzz1 at gmail.com
Wed Dec 30 05:29:29 CET 2015


Dear Justin,


Thanks very much.


Regards

Samith


On Wed, Dec 30, 2015 at 7:58 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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