[gmx-users] Jump of drug to other side of lipid bilayer

Mark Abraham mark.j.abraham at gmail.com
Fri Jul 31 18:27:31 CEST 2015


I answered this question yesterday. Please check for replies and do not
blindly re-post.


On Fri, 31 Jul 2015 08:51 Marzieh Saeedi Masineh <msaeedi at mail.kntu.ac.ir>

> Dear,I have done a simulation of DMPC lipid bilayer for 50 ns which has 10
> drug molecules which were positioned in the water phase in the beginning of
> simulation. In the first 10 ns of simulation, one of the drug molecules
> diffuses from water into the other side of lipid bilayer and remains
> there.  I applied (trjconv –pbc mol),  (trjconv –pbc res), ( trjconv –pbc
> atom) , and (trjconv –center this molecule) to turn back this molecule to
> the first side of lipid bilayer. After that I analyzed the distance of this
> molecule from the center of mass of lipid bilayer that was attached. As you
> can see, the molecule jumps to other side of bilayer and it doesn’t correct
> though –pbc command. What should I do to fix it?Thanks in advance for any
> help,Marzieh,--
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