In a recent benchmark by Piggot, Piñeiro and Khalid (
http://pubs.acs.org/doi/abs/10.1021/ct3003157 ), they showed that the
TIP3P flavour may affect some properties (ApL) for simulations with
CHARM36, concluding that CHARMM-TIP3P is recommended, at least for DPPC.
I've also experienced similar issues with DMPC.
Javier
El 08/07/13 09:29, Albert escribió:
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
--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
--
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
