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
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