Dear all, I have used the PULL code in gmx 4 to unwind part of my protein. 10 runs were performed (all pulling the pulled group from 1.3 nm to 4.3 nm away from the reference). The output seems ok from the pullx.xvg and the trajectories. However, when using g_wham to obtain the PMF there seems to be a problem.
The options for pulling in the mdp file: ; PULLING STUFF pull = umbrella pull_geometry = distance pull_dim = n y n pull_start = yes pull_init1 = 0.0 pull_vec1 = 0.0 1.0 0.0 pull_rate1 = 0.005 pull_ngroups = 1 pull_group0 = Glu33 pull_group1 = Glu81 pull_k1 = 5000 pull_nstxout = 500 pull_nstfout = 500 Using the command (with all the files where they should be) g_wham -ix -it -o -hist results in the following: @ title "Umbrella potential" @ xaxis label "z" @ yaxis label "E (kJ mol\S-1\N)" @TYPE xy 1.324382e+00 0.000000e+00 1.338367e+00 0.000000e+00 1.352352e+00 0.000000e+00 1.366337e+00 0.000000e+00 .... 2.401216e+00 -1.638628e+03 2.415201e+00 -1.730001e+03 2.429185e+00 0.000000e+00 2.443170e+00 -inf 2.457155e+00 -inf 2.471140e+00 -inf 2.485125e+00 -inf 2.499110e+00 -inf 2.513095e+00 -inf ....etc Using the command (with all the files where they should be) g_wham -if -it -o -hist results in a more reasonable plot. However, I don't understand what is on the x-axis. I would expect the reaction coordinate (so distance between pulled and reference groups) there, but this doesn't seem to be the case. I a post of a very similar problem in the mailing list archive of April 2009. It seems, however, that nobody has answered it. I wondered if anyone has a solution to it now? Thanks, Marieke
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