From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Nov 22 2011 - 08:05:08 CST
On Tue, Nov 22, 2011 at 7:21 AM, Molecular Dynamics
<moleculardynamics_at_yahoo.com> wrote:
> Dear Namd users,
>
> I want to run md simulations for binary mixtures consisting of X and Y type
> molecules. I have some questions about generating topology and parameter
> files. Is it possible to model the molecule X in the mixture with united
> atom representation that treats –CHx groups as single interacting site and
> the molecule Y with all atom representation that treats each atom as a
> site in CHARMM19 force field?
possible: yes. meaningful: perhaps, but you have to find that out for yourself.
all that a classical MD code sees are a bunch of coordinates with associated
masses, charges and potentials. it doesn't care at all what it represents all
the MD code does is evaluate the potentials. the rest is up to the user and
follows the simple rule: garbage in, garbage out.
cheers,
axel.
>
> Thanks for your help.
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA.
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