Dear GMXers, I'm running umbrella PMF calculations using GROMACS 4.5. A molecule is placed at various locations of a channel to compute the energy barrier of the entrance.
Below is the PMF section of mdp input, to compute the PMF around the position of (4.04700, 4.0582, -2.2058). The pulling molecule is initially placed close to the (4.04700, 4.0582, -2.2058) position. The box size is 8.094*8.1164*6.0. The series of positions I considered is in the z-coordinate range of -2.2 to -0.8. ----------------------- pull = umbrella pull_geometry = position pull_dim = N N Y pull_start = no pull_ngroups = 1 pull_group0 = pull_group1 = MOL1 pull_init1 = 4.04700 4.05820 -2.2058 pull_rate1 = 0.00 pull_k1 = 1000 pull_nstxout = 1000 pull_nstfout = 1000 ----------------------- For this particular configuration, should I use "pull-geometry=position" or "pull-geometry=distance"? Or they are the same for this case? I read the manual and PMF tutorial but cannot figure this out. Could anyone provide more details about this? Thank you. Best, Yanbin
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