I update the post to say that we tried to make a rerun of the trajectory on our local machine and the output of the pullx.xvg file (created with the option -px of mdrun) is:
************************************************ # This file was created Wed Jun 5 12:15:49 2013 # by the following command: # mdrun -s ../conf10.tpr -rerun ../conf10.xtc -px pullx_conf10.xvg -pf pullf_conf10.xvg -nt 6 -v # # mdrun is part of G R O M A C S: # # Gravel Rubs Often Many Awfully Cauterized Sores # @ 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 3.47835 5.10501 11.644 -0.378345 1.13499 1.73604 20.0000 3.47852 5.12016 11.6554 -0.446518 1.07184 1.69255 40.0000 3.49803 5.12013 11.6612 -0.350032 1.12387 1.75475 (...) ********************************************** The output of the pullx.xvg file is indeed the distance between the two pull groups, but this is very different numbers than the one obtained during the simulation on a cluster (see above post). So the question stand what are the numbers given in the pullx.xvg file created during the original simulation ? -- View this message in context: http://gromacs.5086.x6.nabble.com/pullx-file-content-with-pull-geometry-position-tp5008797p5008850.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