Dear Gromacs users: I am trying cylinder pulling as an option of umbrella sampling using gromacs 4.0.7. Things seem to work but I noticed that in the output file pullx.xvg, the referece group's postion is always 0. I don't think it is right. When I use position pulling, the reference position is never 0.
Thanks for you help. Kun Below is my .mdp file pull = umbrella pull_geometry = cylinder pull_r1 = 1.0 Pull_r0 = 1.0 pull_dim = N N Y pull_start = yes pull_init1 = 0.0 pull_ngroups = 1 pull_group0 = group0 pull_group1 = group1 pull_rate1 = 0.01 pull_vec1 = 0.0 0.0 -1.0 pull_k1 = 3000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 pull_nstfout = 1000 Here is the 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 "0 Z" @ s1 legend "1 dZ" 0.0000 0 5.69818 2.0000 0 5.67685 4.0000 0 5.68564 6.0000 0 5.65461 8.0000 0 5.63482 10.0000 0 5.61658 12.0000 0 5.61679 14.0000 0 5.54434 16.0000 0 5.55352 18.0000 0 5.4964
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