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

Marzieh Saeedi Masineh msaeedi at mail.kntu.ac.ir
Fri Jul 31 08:51:19 CEST 2015

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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