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=23422#Post23422
http://pubs.acs.org/doi/full/10.1021/ct900549r
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),
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
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