[gmx-users] Regarding restricting to centre of box, cos theta functions
Dilip H N
cy16f01.dilip at nitk.edu.in
Thu Apr 6 22:10:11 CEST 2017
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
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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:
>> 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 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
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With Best Regards,
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