[gmx-users] Jumping to other side of box

Mark Abraham mark.j.abraham at gmail.com
Thu Jul 30 13:35:15 CEST 2015


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However, in this case I think the problem is conceptual. When you are using
periodic boundary conditions, you do not have two sides to the bilayer.
There's one contiguous chunk of water, and of course things diffuse freely
within it.


On Wed, Jul 29, 2015 at 9:55 PM Marzieh Saeedi Masineh <
msaeedi at mail.kntu.ac.ir> wrote:

> 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,
> Marzieh,
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