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

[Javier Cerezo]

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