I mean the number of balls which interact in your unit box. If your system is composed of atoms, than it is atoms. If you have coarse-grained representation of virtual sites, it is a total number of them.
Dr. Vitaly Chaban On Sat, Feb 23, 2013 at 8:23 AM, Elisabeth <katesed...@gmail.com> wrote: > Hi Vitaly, > > When you say interaction site you mean number of atoms in the box? How one > can obtain the interaction sites? > > Thanks > > On 22 February 2013 05:04, Dr. Vitaly Chaban <vvcha...@gmail.com> wrote: >> >> >why for a binary >> > (solute+solvent) the size should be larger than 2 Rc? I thought minimum >> > image convention works for all atoms (solute ans solvent) and this makes >> > sure forces are not double-counted. What if the solute is a polymer, I >> > mean >> > how can one calculate diameter of a long chain? >> >> >> If the box size is NOT larger than 2Rc than Rc is larger than a half >> of the box. If it is larger than a half of the box than minimum image >> convention cannot work. >> >> This is not a good idea to use so small box. You will end up with >> methodological problems of some kind eventually. >> >> >> Dr. Vitaly Chaban -- 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
