[gmx-users] Regarding restricting to centre of box, cos theta functions
jalemkul at vt.edu
Thu Apr 6 21:02:41 CEST 2017
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
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
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