Hi every one I used below pull-code to pull one of molecules in my system, but I am a little bit confused about output of the ######################### pull code pull-ngroups = 1 pull-group1-name = sub3 pull-coord1-groups = 0 1 pull-coord1-origin = 0 0 0 pull-coord1-vec = 0 0 1 pull-coord1-dim = N N Y pull-coord1-geometry = direction pull-coord1-type = umbrella ##############################
output @ title "Pull COM" @ xaxis label "Time (ps)" @ yaxis label "Position (nm)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "1" @ s1 legend "1 ref" @ s2 legend "1 dZ" @ s3 legend "1 g 1 Z" @ s4 legend "1 g 2 Z" 0.0000 4.19706 4.19706 4.19706 0 4.19706 1.0000 4.19496 4.20306 4.19496 0 4.19496 2.0000 4.20191 4.20906 4.20191 0 4.20191 3.0000 4.19645 4.21506 4.19645 0 4.19645 ################################### The first column is the time, and I guess the the second is z coordinate of the "sub3" according to the "s0 legend "1"", and the third is the distance between the "sub3" and the reference. But, what does the rest of the columns mean? Another question is if I output the force via rerun and energy group to calculate the force between the "sub3" and other molecules, will the force exerted by the spring be included, or just the non-bond force between "sub3" and other molecules will be included? Fan -- 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.
