[gmx-users] Re: System size and minimum image convention
katesedate at gmail.com
Sat Feb 23 08:23:45 CET 2013
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
> > 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
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