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 jalem...@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-requ...@gromacs.org.
