[gmx-users] constraining CoM of two proteins individually

[Justin Lemkul]

On 2/9/17 2:22 PM, Irem Altan wrote:
> Thanks. In that case, is it possible to use a flat-bottomed potential?
>

Yes.

http://manual.gromacs.org/documentation/2016.2/user-guide/mdp-options.html#com-pulling

-Justin

> Best,
> Irem
>
>> On Feb 6, 2017, at 1:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>> On 2/6/17 10:06 AM, Irem Altan wrote:
>>> Hi,
>>>
>>> I have a system that consists of two proteins separated by a certain distance. I want to keep this distance constant by constraining the center of mass of the two proteins individually. How can I do this?
>>>
>>
>> If you just want to maintain a distance, use a biasing potential via the pull code.
>>
>> -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
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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

==================================================