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
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
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.
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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