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.,) ..??
<https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22> 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 > > -- > ================================================== > > 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. > -- With Best Regards, DILIP.H.N Ph.D Student -- 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.