[gmx-users] Re: System size and minimum image convention

Elisabeth katesedate at gmail.com
Sat Feb 23 08:23:45 CET 2013

Hi Vitaly,

When you say interaction site you mean number of atoms in the box? How one
can obtain the interaction sites?


On 22 February 2013 05:04, Dr. Vitaly Chaban <vvchaban at 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 at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list