[gmx-users] tip3p

[Chetan Mahajan]

Hi Mark,

Thanks for the reply. Now, 1983 article by Jorgensen gives parameters for
rigid tip3p, whereas I am seeking that for flexible tip3p. Force constant
is not mentioned in 1983 article by Jorgensen. The article that I cited in
#1 point below gives these parameters for modified tip3p. I do not
understand why these are different from those in tip3p files in gromacs
installed. Is there any other article describing flexible tip3p parameters?

Thanks
Chetan


On Sun, Mar 9, 2014 at 7:33 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> On Sun, Mar 9, 2014 at 1:00 PM, Chetan Mahajan <chetanvm10 at gmail.com>
> wrote:
>
> > Hi All
> >
> > I have tip3p water potential parameters from 3 different sources and they
> > differ quite substantially. I tried finding answer on the web or manual,
> > but no success.
> > Following lists all the three sources and bond potential force constant
> > (kb) value, in bracket as an example of how values differ in all the
> three
> > sources.
> >
> > 1. From the article: Neria, E.; Fischer, S.; Karplus, M. J. Chem. Phys.
> > 1996, 105, 1902. (kb= 450 kcal/(mol.A02)), where A0 is angstrom. ( in
> > Gromacs units,
> > kb=188280 kcal/(mol.A02))
> >
>
> This is not the TIP3P citation (see gromacs manual), and as you can see in
> the penultimate paragraph, it does not even use the standard TIP3P.
>
> 2. From tip3p files in forcefield directories in
> > gromacs/4.6.3/share/gromacs/top
> > (502416.0 kJ/(mol.nm2)
> >
>
> This agrees with Jorgensen 1983
>
>
> > 3. That used by acpype tool while converting amber input files to gromacs
> > input files.( 462750.4 kJ/(mol.nm2))
> >
>
> No idea where this is from or what it is doing, but presumably reading the
> documentation or code will be a good start! :-)
>
> Mark
>
>
> > 2 and 3 force constant units should conform to Gromacs, so kJ and nm.
> >
> > It's very confusing, surprising and disappointing why these three values
> > differ so much. What is the correct value and why? I really appreciate
> your
> > response.
> >
> > Thanks
> > Chetan
> > --
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