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? Many thanks in advance. Regards, Jennifer -- 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.
