Dear GMXers,<br><br>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.<br><br>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. <br>
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.<br><br>-----------------------<br>pull = umbrella<br>pull_geometry = position<br>pull_dim = N N Y<br>
pull_start = no <br>pull_ngroups = 1<br>pull_group0 = <br>pull_group1 = MOL1<br>pull_init1 = 4.04700 4.05820 -2.2058<br>pull_rate1 = 0.00 <br>pull_k1 = 1000 <br>pull_nstxout = 1000<br>
pull_nstfout = 1000<br>-----------------------<br><br>For this particular configuration, should I use "pull-geometry=position" or "pull-geometry=distance"? Or they are the same for this case?<br>I read the manual and PMF tutorial but cannot figure this out. Could anyone provide more details about this?<br>
<br>Thank you.<br><br>Best,<br>Yanbin<br>