[gmx-users] Umbrella sampling PMF using pull-geometry=direction

Pradyumn Sharma cherpradyumnsharma at gmail.com
Fri May 17 13:33:50 CEST 2019

Dear all
I am trying to get a PMF for a small molecule translocation through an
asymmetric membrane. I am doing it using pull-geometry= direction to do
umbrella sampling at each window. I am getting a profile in which PMF of
molecule in the bulk water at one side of the membrane is different from
the one in bulk water on the other side, which should not be the case
because it is bulk water on both sides. I saw the trajectory, as well as my
density map, both shows that windows at either end are corresponding to the
position of molecule in bulk water.
I am giving a link for files related including:

a. MDP file - for one window
b. Density map for water along the z-direction, where 0 represents my
membrane centre
c. PMF profile

Am I interpreting this correctly? if some mistake is there in parameters or
my interpretation kindly let me know.

Additional details:
1. I am using gromacs-2018.2.
2. I got the initial system. from CHARMMGUI.
3. Proper overlapping is there I checked my histograms, also if that was
the case than PMF would not have been so smooth.
3. I already did US simulations for symmetric membrane with
pull-geometry=distance, also I have reproduced results in the literature
Pradyumn Sharma
PhD Student
Department of Chemical Engineering
Indian Institute Of Science (IISc)

More information about the gromacs.org_gmx-users mailing list