[gmx-users] Prevent protein rotation - rectangular box

[Steven Neumann]

Thanks but it will take some time to install 5.0 on the cluster. How about
[ angle_restraints_z ]? I could think of an atom in the protein to restrain
along z axis (protein length). Not sure how can I measure such an angle
though and which atom to choose.



On Tue, Jun 3, 2014 at 9:21 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/2/14, 9:15 PM, Steven Neumann 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?
>>
>>
> A flat-bottom restraint would probably accomplish the same thing, applying
> a restraint in the dimensions perpendicular to the long axis.  The
> flat-bottom potential is supported as of the first beta release of 5.0.
>
> -Justin
>
>
> --
> ==================================================
>
> 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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