Thanks for the help. Just to clarify, amber in no way changes the SPC/e or
tip3p paramaters during the overall force field parameters determination,
correct? I am just trying to rationalize in my head how it is possible to
simulate using OPLS/TIP3P and amber/TIP3p if the mixing rule are different
but the water force field parameters are the same. Perhaps the force field
themselves were determined via parameter optimization in conjunction with
the tip3p model and SPC/E model. Can anyone clarify if this is the case for
amber? I am looking in the GAFF file, but I don't see any reference to
SPC/e water atoms. However, in the mod4 section the epsilon value for
oxygen is 0.1520, but I believe the original 1983 paper had it as 0.1521.
Just trying to make sure I am not missing something.
On Sun, Oct 4, 2015 at 1:27 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Sun, Oct 4, 2015 at 12:14 AM, conor parks <coparks2012.gmail.com>
> wrote:
>
> > hello,
> >
> > I am interested in using either the tip3p or SPC/e water models in a
> > glycine simulation I am trying to perform. However, I am slightly
> confused
> > about the mixing rules between atom pairs for the water molecules. Amber
> > uses an arithmetic average to generate the epsilon sigma pairs. OPLS, on
> > the other hand, uses geometric averages. However, I see people simulating
> > using amber with tip3p, and other instances using OPLS with tip3p.What is
> > the appropriate mixing rule for these various water models when I am
> > simulating the rest of my system using the amber force field?
> >
>
> The mixing rules are Lorentz-Berthelot (i.e., geometric mean for epsilon
> and
> arithmetic mean for sigma). This is the case with all TIPnP and SPCE water
> models in Amber (and, I believe, in CHARMM as well).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
B.S.E in Chemical Engineering, University of Michigan, 2012
PhD candidate in Chemical Engineering, Purdue University
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Received on Sun Oct 04 2015 - 00:00:04 PDT
