Thank you, Justin. Jennifer
On Tue, Jun 2, 2015 at 2:09 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/2/15 5:01 AM, Jennifer Vo wrote: > >> Dear All, >> I used g_hbond to analyze the possible hydrogen bonds between protein and >> solvent (water) over the trajectory with this command: >> g_hbond -s md-1.tpr -f md.xtc -n index.ndx -hbm hbmap.xpm -num hbnum.xvg >> -g >> hbond.log -dist hbdist.xvg -nhbdist nhbdist.xvg >> >> The log file showed me: >> .... >> SER141OG SER141HG SOL2920OW >> SER141OG SER141HG SOL4449OW >> SER141OG SER141HG SOL5073OW >> SER141OG SER141HG SOL11886OW >> SER141OG SER141HG SOL13715OW >> .... >> I wonder if this calculation is based on one coordinate file (if yes, >> which >> one!?) or the average structure over trajectory? >> > > Trajectory analysis is done for every frame in the trajectory. The log > output just indicates that different waters were hydrogen bonded to that > particular Ser at different times. > > -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. > -- 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.