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 -------------------------- 叶国东，博士，教授 广州医科大学 药学院 化学教研室 广州市番禺区新造镇 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
