Hi Lin, 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. Cheers, Tsjerk On Tue, Oct 8, 2013 at 7:30 PM, Chih-Ying Lin <chihying2...@gmail.com>wrote: > Hello, > 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 "The simulations described here rely on an outdated force field (Gromos 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 Is the force field Gromos 45a3 outdated?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 > Lin > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
