[gmx-developers] Contributing new water models
mark.j.abraham at gmail.com
Fri May 30 09:34:47 CEST 2014
That sounds useful. Generally we will only incorporate force field things
that are published, so that is good. I'm hesitant to make them available
with pdb2gmx -water, lest it be too easy for people to misuse them with an
inappropriate force field. Incorporating the atom types into the tested
force fields and making the .itp files available with them sounds fine to
me. Then a quick sed -i will replace whatever was selected with pdb2gmx.
On May 28, 2014 7:12 PM, "Lee-Ping Wang" <leeping at stanford.edu> wrote:
> Dear developers,
> I'd like to contribute the following water models that were published in
> our recent article, "Building force fields - a systematic, automatic and
> reproducible approach." The models, called TIP3P-FB and TIP4P-FB, are
> reparameterized versions of the TIP3P and TIP4P models; they have identical
> functional forms and computational cost, just different parameters. They
> are highly accurate for reproducing the thermodynamic, kinetic and
> structural properties of liquid water across a wide temperature and
> pressure range. The .itp files are attached in their final form.
> I've run several microseconds of protein simulations using TIP3P-FB and
> TIP4P-FB, and they are highly compatible with the AMBER protein force
> fields (more specifically, amber99sb, amber99sb-ildn and amber99sb-nmr).
> In fact, replacing TIP3P with TIP3P-FB tends to improve the stability of
> the "fast folding" proteins in D.E. Shaw's paper, and it also improves the
> prediction of NMR J-couplings and chemical shifts. This is currently
> unpublished work but I'm working on a manuscript.
> Please let me know if there's interest. I think it could make sense to
> bundle this with the main Gromacs distribution, because the water models
> come with atom types that need to go into "ffnonbonded.itp" for the various
> implemented force fields.
> - Lee-Ping Wang
> Link to the paper:
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