[gmx-users] Prevent protein rotation - rectangular box

[Justin Lemkul]

On 6/2/14, 9:43 PM, Steven Neumann wrote:
> 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.
>

Possibly, but I've never tried using anything like that.  The flat-bottom 
potential is effectively the same as reflective boundary conditions that nearly 
all simulation software has used for a very long time.  No need to reinvent the 
wheel.

As an aside, you can always install custom software within your own $HOME 
directory, unless the cluster has some weird rules about not running things from 
$HOME.  No need to bug a sysadmin, in most cases :)

-Justin

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

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

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