Dear Chris, Thank you for your directions. NaCl concentration in my system is 0.14 M and I often visualize the whole system and can see the ions around the system but not in crystal form! Well, it sounds really strange to me! And I don't know if I proceed with such a system, I get scientific results or not?! I appreciate your further helps.
Best Regards Arman On Tue, Oct 30, 2012 at 4:39 AM, Christopher Neale < chris.ne...@mail.utoronto.ca> wrote: > 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 > -- 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
