Dear Friends, Thank you for your kind and informative responses. As Dr. Chaban noted, I checked the density and it was roughly 880 gr.cm-3 which seems low!
I greatly appreciate your further helps. Best Wishes Arman On Mon, Oct 29, 2012 at 1:20 PM, Dr. Vitaly Chaban <vvcha...@gmail.com>wrote: > >> On 10/26/12 3:25 PM, Arman M. Soufiani wrote: > >> > Dear Gromacs users, > >> > > >> > 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. > >> > > >> > >> That sounds very odd, but perhaps your unit cell is not sufficiently > >> solvated to > >> start with. If you have voids, you may have available volume. > >> > >> -Justin > > > You must compare the simulated density with the experimental density. > > There is no other way to conclude if your holes are genuine or not in > this kind of matter. > > > Dr. Vitaly V. Chaban > MEMPHYS - Center for Biomembrane Physics > Department of Physics, Chemistry and Pharmacy > University of Southern Denmark > Campusvej 55, 5230 Odense M, Denmark > -- > 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
