[gmx-users] Prevent protein rotation - rectangular box

[Steven Neumann]

The version provided does not support GPUs... Is there any version with
rotational restraints implemented?


On Tue, Jun 3, 2014 at 9:15 AM, Steven Neumann <s.neumann08 at gmail.com>
wrote:

>
>
>
> On Mon, Jun 2, 2014 at 8:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/2/14, 7:10 AM, Steven Neumann wrote:
>>
>>> Dear Users,
>>>
>>> I am trying to prevent rotation of my protein in recatngular box and I am
>>> thinking about applying some position restraints with the dummy atoms. I
>>> read some posts about this subject from 2003, 2006 but nothing recent. Is
>>>
>>
>> Rather than risk wasting time by repeating things, if you're looking up
>> information in old posts, please provide the links to those posts for
>> context.
>
>
>
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2006-July/022914.html
>
>>
>>
>>  there a gromacs tool to create a dummy atom a apply position restraints
>>> or
>>> maybe a pull_code would be a solution? Please, provide me with some
>>> information.
>>>
>>>
>> You can restrain whatever you like, and I don't necessarily see the need
>> for a dummy atom in this case, but the larger question is - why do you need
>> to prevent rotation?
>>
>> -Justin
>>
>
>
> I am studying protein in water. In the dodecahedron box I would have 80K
> water molecules which on my GPU machine give 6 ns/day. If I place my
> protein to the triclinic box I would get 20K atoms getting 50 ns/day. Thats
> a significant improvement. My protein in 15 nm long and 4 nm width so it is
> likely it can rotate and interact with its periodic image. I wish to
> prevent the rotational movements. Would you suggest something?
>
>
> Setven
>
>
>
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> 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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>
>