[gmx-users] Jumping to other side of box

Marzieh Saeedi Masineh msaeedi at mail.kntu.ac.ir
Wed Jul 29 21:55:30 CEST 2015

Dear Users, 

I have done a simulation of DMPC lipid bilayer which has 10 drug molecules in the water phase for 50 ns. 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. It 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, 


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