hello justin i have been visualized the file of confout.gro file in vmd and the position of protein and ligand is ok i know i have to analyze all the parameters like energy and rmsd is it sufficient to extend my simulation or which file i have to visualized
On Tue, Oct 14, 2014 at 5:25 PM, Justin Lemkul <[email protected]> wrote: > > > On 10/14/14 12:31 AM, RINU KHATTRI wrote: >> >> hello gromacs user i am working on protein ligand complex with popc >> membrane >> i am running production md in extended time (40 ns) i got some file i >> am using -noappend option i got confout.gro file in each extended time >> what is the use of this file if i want see my protein or ligand are in >> proper place this confout.gro is sufficient of i have to see traj >> file > > > The confout.gro file is simply the last snapshot of the simulation interval. > Whether or not it is reflective of the dynamics during that interval is > unknown without doing analysis and simple visualization. > > -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 > > [email protected] | (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 [email protected]. -- 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 [email protected].
