Thanks Justin. Can you please elaborate on 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?
Thanks in advance, On 21 February 2013 18:16, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/21/13 6:10 PM, Elisabeth wrote: > >> Hello everyone, >> >> Does anyone know if the minimum image convention has something to do with >> the box size effect (independence of simulation results from system size) >> ? >> i.e. When the box size is larger than 2*r_c, does this ensure that the >> results are independent of size pf the system (number of atoms in box)? >> >> Please guide me if I am confusing these two issues with each other, >> >> > The finite size effect and minimum image convention are different. The > minimum image convention simply says that your molecules should not have > their forces double-counted through interactions in the central unit cell > and a neighboring one. That leads to spurious dynamics. A box of 2*r_c is > an absolute minimum, but if there is a solute involved (i.e. not pure > solvent) then your box must be larger (diameter of solute + 2*r_c). > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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