VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 26 2009 - 08:48:24 CDT

On Mon, 2009-10-26 at 14:48 +0200, politr_at_huji.ac.il wrote:

hi regina,

> Hi to All,
> I want to run simulation of peptide by using SPC/E water model .
> How can I solvate peptide by VMD with SPC/E water? And where can I
> get
> topology and parameter files which include SPC/E water? Thanks to all

first of all, i hope that you are aware of the implications, that
using a different water potential with force field parameters that
were not parametrized with that water potential in mind, i.e. that
that you destroy the "balance" between peptide solvation and
peptide-peptide interaction.

secondly, the best way to proceed is to first generate an equilibrated
water box with SPC/E water. as you can see from the parameters listed
at: http://en.wikipedia.org/wiki/Water_model
SPC/E has a different geometry than TIP3P (n.b. the TIP3P in CHARMM
is not really TIP3P). then create a copy of your parameter file and
modify the water parameters in it, that would allow you to run the
simulation.

but as mentioned before, you would have to re-parametrize everything
else to have a properly balanced force field, so please be _very_
careful to not overinterpret the results. particularly, using SPC/E
with CHARMM parameters can be tricky, since SPC/E doesn't have the
(mostly repulsive) lennard jones term on water hydrogens and even
large point charges that are further away from the center, so that
coulomb interactions between SPC/E and peptide atoms will be
significantly enhanced.

cheers,
   axel.

> people who answer to the questions and thank you in advance for answer
> to this particular question.
>
> Regina
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.