[gmx-users] Is Gromos force field 45a3 out of dated?
tsjerkw at gmail.com
Tue Oct 8 22:06:40 CEST 2013
I would say that it is not correct to call 45a3 deprecated. Like other
force fields, GROMOS 45a3 is also the result of careful parameterization.
The later GROMOS forcefields 53a5, 53a6, 54a7 and 54a8, took of a
completely different approach in parameterization, and are in that respect
not so much superseding, but rather complementary. Personally, I have been
and am still suspicious regarding these newer force fields, possibly with
the exception of 54a8. In 2006 I performed a statistical comparison of
simulations performed with 43a2 (overall similar to 45a3), and we found
that there were differences that could be related to the number of charged
residues. These residues were not reparameterized between 45a3 and 53a6,
which means that 53a6 (and 54a7) actually consists of a part which was
reparameterized and a part which was not, or at least not against the free
enthalpy of solvation. The consequence of this was that the new force field
was not consistent and could give rise to larger RMSD values and larger
radii of gyration, with the extent correlating with the number of charged
residues. This can be turned around: 45a3 is likely to give more stable
structures than the newer force fields and it is improbable that 45a3 would
give partial unfolding as artifact.
For the newest version, 54a8, the charged residues have also been
reparameterized and the result set should be consistent again.
I hope this is of some use to you.
On Tue, Oct 8, 2013 at 7:30 PM, Chih-Ying Lin <chihying2008 at gmail.com>wrote:
> I submitted a paper and get rejected immediately by editor because of the
> following comment.
> "The simulations described here rely on an outdated force field (Gromos
> 45a3) and I suspect that the partial unfolding described here is at least
> in part due to force field artifacts. "
> Our simulation work fit the results from the experimental work quite well
> but the editor returned his suspicion.
> Is the force field Gromos 45a3 outdated?
> Could anyone refer me more details about the force field of Gromos 45a3?
> Could anyone refer me about any cases of the broken simulation from the
> force field artifacts?
> Thank you
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Tsjerk A. Wassenaar, Ph.D.
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