[gmx-users] why TIPS3P, why not TIP3P?

Mark Abraham mark.j.abraham at gmail.com
Mon Jul 8 09:42:05 CEST 2013

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" <mailmd2011 at 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
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