CHARMM36 is a user contribution, so you should be sure to contact its author for the reason / a fix. Personally, I agree with the consensus that LJ on H is not necessary. On Jul 8, 2013 9:30 AM, "Albert" <mailmd2...@gmail.com> wrote:
> Hello: > > I noticed that the CHARMM36 FF recommend CHARMM TIP 3-point with LJ on > H's model for lipids when we run pb2gmx each time. I am just wondering, why > it is recommend for lipids? Is there any special superior reason to do so? > As far as I google both Gromacs maillist and CHARMM forum, most people > conclude that there is no big differences between CHARMM TIP3 model and > original TIP3P model. Here is what I found: > > > http://www.charmm.org/**ubbthreads/ubbthreads.php?ubb=** > showflat&Number=23727<http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=23727> > > http://www.charmm.org/**ubbthreads/ubbthreads.php?ubb=** > showflat&Number=23422#**Post23422<http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=23422#Post23422> > > http://pubs.acs.org/doi/full/**10.1021/ct900549r<http://pubs.acs.org/doi/full/10.1021/ct900549r> > > http://lists.gromacs.org/**pipermail/gmx-users/2010-** > September/053966.html<http://lists.gromacs.org/pipermail/gmx-users/2010-September/053966.html> > > Actually, in one of the recent De.Shaw CELL paper ( > http://www.sciencedirect.com/**science/article/pii/**S0092867412015528<http://www.sciencedirect.com/science/article/pii/S0092867412015528>), > they also introduced normal TIP3P water model+ CHARMM36 FF for their > system. In this work, they performed 100+ us long time scaled MD simulation > for a extremely large membrane protein. > > could anybody comment on this issue? > > THX a lot. > > Albert > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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