Dear Mark Very thanks for your reply
> To make this clear, center the trajectory on the water and watch the > time evolution in some visualization program. I did your suggestion (center the trajectory on the water). Again, drug molecule is in region (1)in some frames and is in region (4) in other frames. ---------------------------------------------------------------------------------- Dear Justin Very thanks for your attention > As has already been stated several times, there is no problem at all. > The outcome is completely normal, and there are not discrete > regions (1) and (4). > It is a continuous block of water via PBC. The molecule can freely > diffuse throughout it. If outcome is completely normal, Can I use this structure for pmf calculation. I want to calculate potential of mean force, delta G, as a function of the distance between the centers of mass of drug and the centers of mass of bilayer. Best wishes for you. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
