[gmx-users] The PMF curve is asymmetric (However many results of membrane penetration are symmetric)

ygdcn ygdcn at 163.com
Fri Feb 23 04:41:33 CET 2018

Hi all: 
I tried to use MD simulation to pull a drug across the POPC membrane and to calculate PMF. I obtained the PMF curve following the guide (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/) 
I found the PMF curve increases as the penetration process proceeds. The PMF curve is asymmetric, it increases in the whole time. However many results of membrane penetration are symmetric, e.g. increase earlier and decrease lately (X=0 in the central) . How can I get the similar result? There are examples of this in the GROMACS manual (see, e.g. the diagram for the cylinder geometry in the case of layered systems), but it is too difficult for me to understand it. I also read the answer (https://www.researchgate.net/post/How_to_pull_a_solute_across_liquid-liquid_interface).  I am sure that a drug and a membrane will come closer when I used the negative pull rate. But I have some doubts whether the drug can continue to move ahead and leave the membrane after it arrive at the central of membrane.

Best regards, 

Best regards, 
祝  安好
Guodong YE 
Ph.D,  Professor
Department of Pharmaceutical Chemistry
School of Pharmaceutical Sciences
Guangzhou Medical University
Address: Guangzhou Medical University (Panyu Campus) 
Xinzao Town, Panyu District, Guangzhou, China, 511436
广州医科大学 药学院 化学教研室

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