Hi Albert
I've been using the version dated July 2010, which seems to be the last
one on the user contribution section.
I pointed the paper by Piggot and co-workers to add a point on your
original question whether CHARM-TIP3P makes a difference or not. I think
that the paper answer why the developer of the FF contribution recommend
such water model.
Using it or not is of course up to the user and may be affected by the
system and settings (my own experience is with bilayer only systems,
membrane proteins may behave quite different). And I agree with you that
the extra computational burden imposed by CHARM-TIP3P is something that
encourages one to use the standard TIP3P, if it provides the correct
answers. For instance, in the aforementioned paper, it seems that POPC
is not so affected as DPPC.
Javier
El 08/07/13 11:25, Albert escribió:
On 07/08/2013 10:47 AM, Javier Cerezo wrote:
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
which CHARMM36 FF do you use? The CHARMM36 is being update from time
to time.
It may have some influence on the head property of the lipids, but how
much it would be for the whole protein/membrane system, it is still
unclear. For the long time scaled MD simulations, many people would be
hesitated to introducing charmm-TIP3P which sacrifice too much speed.....
I've also observed that in several paper, people said Na+ have
influence on POPC property similar to your claims, but most people
still prefer to use POPC+0.15M NaCl which is the most close system to
physiology environment.
Albert
--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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