Dear gromacs user, I run a simulation where I restrain two groups in a specific position with respect to one another: one is part of a protein (index group name: pull_group) the other is just one ion (index pull_group name r_60022). I have the following parameters in my mdp file:
********************************* ; Pull code pull = umbrella pull_geometry = position ; pull_dim = Y Y Y pull_start = no pull_ngroups = 1 pull_group0 = pull_group pull_group1 = r_60022 pull_init1 = -.4110 1.0700 1.7760 pull_rate1 = 0.0 pull_vec1 = -0.264 0.315 0.912 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 100 ; every 0.2 ps pull_nstfout = 100 ; every 0.2 ps ********************************** So the ion should be restrained around the position pull_init1 with respect to the center of mass of the protein. Here is a sample of the obtained pullx.xvg file: ********************************** @ 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 "0 X" @ s1 legend "0 Y" @ s2 legend "0 Z" @ s3 legend "1 dX" @ s4 legend "1 dY" @ s5 legend "1 dZ" 0.0000 3.43102 5.2156 11.5301 -0.531018 1.0244 2.13988 0.2000 3.43096 5.21543 11.53 -0.544007 1.02157 2.14952 0.4000 3.43094 5.2146 11.5304 -0.551138 1.00177 2.12238 0.6000 3.43074 5.21354 11.5312 -0.559285 1.01417 2.13649 (...) 20.0000 3.45331 5.22215 11.51 -0.646908 0.939066 2.11768 (...) 40.0000 3.45141 5.21115 11.5685 -0.689742 0.978908 2.14589 (...) ***************************************** As far as I understood the manual and after searching the forum I though that the first column is the time, the next three columns the position of the pulled group (r_60022) at the time and the last three columns the distance in the x y z direction between the reference group (pull_group, bad name choice I know) and the pulled group (r_60022). If that was true it would suggest that the ion is pulled more than three A away from the center of the umbrella potential. After checking the trajectory visually and by calculating the distance between pull_group and r_60022 using g_dist on the trajectory we can see it is not the case. Here is a sample of the g_dist output: **************************************** @ title "Distance" @ xaxis label "Time (ps)" @ yaxis label "Distance (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 "|d|" @ s1 legend "d\sx\N" @ s2 legend "d\sy\N" @ s3 legend "d\sz\N" 0.0000000 2.1085827 -0.3782945 1.1350875 1.7362576 20.0000000 2.0527425 -0.4464533 1.0719213 1.6927538 40.0000000 2.1132109 -0.3499784 1.1239562 1.7549639 (...) *************************************** Which oscillate correctly around the pull_init1 vector as defined in the mdp file. More importantly these results are different from the results in the pullx.xvg file (at least the results I expected to have). Can somebody clarify what is actually in the pullx.xvg file ? Best, Bastien Loubet -- View this message in context: http://gromacs.5086.x6.nabble.com/pullx-file-content-with-pull-geometry-position-tp5008797.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
