[gmx-users] Regarding restricting to centre of box, cos theta functions

[Justin Lemkul]

On 4/6/17 4:10 PM, Dilip H N wrote:
> Thank you Justin..
>
> For my query on cos theta distribution functions..
> How can i calculate cos theta distributions (eg.,cos theta distributions of
> hydrogen's of water in first hydration shell layer of amino acid)..??
> Is there any command that i need to give like as in rdf  commands
> (indexing,etc.,)  ..??
>

It sounds like you want to be using gmx sorient.

-Justin

>
>
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> On Fri, Apr 7, 2017 at 12:32 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 4/6/17 2:58 PM, Dilip H N wrote:
>>
>>> Hello,
>>> I have ran a md simulation of amino acid with solvent molecules with it.
>>> During simulation run, the molecules (amino acid, solvent molecules) move
>>> around the box, but i don't want the amino acid to move around during the
>>> simulation, want to fix it to centre of box..
>>> 1] How can i restrict/fix/keep  only the amino acid molecule in/to the
>>> centre of the box during simulation ..? Is it possible..
>>>
>>>
>> It's not necessary.  A simulation with periodic boundary conditions is
>> infinite and therefore there is no center.  If it's inconvenient to
>> visualize, that has no bearing on the physics.  Don't try to perturb the
>> system with biasing potentials; just re-center with trjconv when the
>> simulation is done.
>>
>> 2] How can i calculate the cos theta function in gromacs..??
>>>
>>>
>> Put down GROMACS and pick up a high school trigonometry book.  GROMACS
>> isn't a calculator :)
>>
>> -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
>> 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 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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