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

[Javier Cerezo]

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