In addition to the comments of Dallas Warren, which seems quite possible and should be checked, are you sure that you are seeing real holes and not just salt crystals that look like holes when you render only the waters with VMD? I have found that, at NaCL concentrations above 1 M, lipid bilayers catalyze the formation of salt crystals when using TIP3P/4P water and the OPLS/AA-L force field for ions. These crystals looked a lot like vacuum holes to me until I visualized the salt.
Chris. -- original message -- I am simulating a protein on a polymer surface for further adsorption free energy calculation. However, after performing the NVT run either for short or long durations I found out that couple of holes appear in the physiological saline solution (solvent)!!! Additionally, even proceeding with a long NPT run the holes are still present in the system. I would be thankful if you could direct me what could be source of such a strange outcome. Best Wishes Arman -- 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
