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

Justin Lemkul jalemkul at vt.edu
Thu Apr 6 21:02:41 CEST 2017

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 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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