[gmx-users] Prevent protein rotation - rectangular box

[Steven Neumann]

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



>
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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> Department of Pharmaceutical Sciences
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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