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

[Dilip H N]

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.,)  ..??



  <https://mailtrack.io/> Sent with Mailtrack
<https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22>

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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student