chetanvm10 at gmail.com
Sun Mar 9 22:54:21 CET 2014
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?
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>
> > 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
> > 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! :-)
> > 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
> > response.
> > Thanks
> > Chetan
> > --
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