[gmx-users] System size and minimum image convention

Elisabeth katesedate at gmail.com
Fri Feb 22 00:30:17 CET 2013

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 <jalemkul at 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
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