On Mon, Oct 29, 2012 at 2:38 PM, Arman Mahboubi Soufiani <armansoufi...@gmail.com> wrote: > 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!
Dear Arman - You did not mention the experimental density of your system. Whereas we expect saline solution to exhibit the density of > 1000 kg/m3, we have no idea about your polymer composition and spatial structure. 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 > > 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
