VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun May 24 2015 - 04:06:30 CDT
On Sun, May 24, 2015 at 9:17 AM, Monika Madhavi <monikamadhavi_at_gmail.com> wrote:
> Dear all,
> I want to create a simulation box which only consists of water. I created a
> TIP3p water box using solvate plugin. Now I want to create boxes of
> different water models like SPC,SPCE,TIP4p,TIP5p etc. Can you advise me on
> how to do this? I hope to use charmm force field for all simulations.
this is straightforward to do for all 3-site models, all you need are
adapted topology and parameter files that contain the parameters
suitable for the respective water models, and possibly adjusted names
for atom types and residue names. you can reuse the tip3p water box,
the small differences in the water geometry and liquid structure will
become irrelevant during equilibration.
for tip4p and tip5p you will have to look into how the specific MD
code handles the construction of the mass-less charge site locations.
that would then determine how you will have to build the topology.
please note that you can feed any kind of solvent to it, and that you
can construct a bulk system from a single molecule by replicating it a
few times and then equilibrating it and then repeating this until the
desired size is reached.
> W.A.Monika Madhavi
> Lecturer (Probation),
> Department of Physics,
> University of Colombo.
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.