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