Hello, I have been using the pull code for friction calculations. I am not doing umbrella sampling but just pulling one slab of crystal on top of another with the constant velocity. I would like to know how Gromacs is calculating the pulling force (pullf.xvg) during sliding. Is the pulling force obtained through U = 1/2K(vt-(x-x0))^2 harmonic potential? I am using following parameters:
pull = umbrella pull_geometry = direction_periodic pull_dim = Y Y Y pull_start = yes pull_ngroups = 1 pull_group0 = ICE_A pull_group1 = ICE_B pull_pbcatom0 = 0 pull_pbcatom1 = 0 pull_vec1 = 1 0 0 pull_rate1 = 0.004 pull_k1 = 10000 Since I have pull_start=yes, does it mean that the initial spring length is the COM distance between ICE_A and ICE_B? Another question is regarded to the velocity distribution. I used g_traj to plot the velocity distribution of my system which I compared with the distribution plot calculated from the coordinates and they dont match. The distribution calculated by Gromacs has a tail while my calculations don't show any. Could you please tell me how is it calculated in Gromacs? Thank you for your attention to this matter. Cheers, Nino-- 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