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

[Pradyumn Sharma]

I am sorry I forgot to give the link in the last mail.

https://indianinstituteofscience-my.sharepoint.com/:f:/g/personal/pradyumn_iisc_ac_in/EkAdkzcZsepHvbE1UDJPS5UBg2mENMYsRC2S0Z2DDWS9xQ?e=3GeICo

On Fri, May 17, 2019 at 5:03 PM Pradyumn Sharma <
cherpradyumnsharma at gmail.com> wrote:

> 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
> already.
> --
> Regards
> Pradyumn Sharma
> PhD Student
> Department of Chemical Engineering
> Indian Institute Of Science (IISc)
>


-- 
Regards
Pradyumn Sharma
PhD Student
Department of Chemical Engineering
Indian Institute Of Science (IISc)