Thanks a lot for your answer.
I don't have access yet to pmemd (still waiting for the license over here), so we have to stick to NAMD and with their implementation it makes a huge difference on performance. This is why we still use it.
Best regards.
Peter
-----Message d'origine-----
De : Jason Swails [mailto:jason.swails.gmail.com]
Envoyé : lundi 27 juillet 2015 16:19
À : amber.ambermd.org
Objet : Re: [AMBER] which solvent model to use with solvateCap
On Mon, 2015-07-27 at 11:12 +0000, peter.schmidtke.discngine.servier.com
wrote:
> Dear Amber users,
>
> I would like to use the TIP4P solvent model with the amber force
> field. After some reading I found that using the TIP4P-Ew was
> recommended when running PME simulations.
> However I also run non periodic simulations (using solvateCap in tleap
> to create for instance a solvent sphere that I constrain later in the
> simulation). Can I also use the same water parameters (TIP4P-Ew) for
> such simulations or shall I switch to normal TIP4P in this case?
Solvent caps are not frequently used for much anymore. (The newest paper I saw from Google Scholar matching "solvent cap molecular dynamics" was from 2001.) PME is often cheaper for large systems even if you need more water than the solvent cap by virtue of using a O(N
logN) algorithm instead of a O(N^2) one. Add in the fact that neither pmemd.cuda nor pmemd/pmemd.MPI are capable of running with a solvent cap, and it's even more likely from a practical perspective for PME to actually be *faster* than a solvent cap simulation (pmemd.cuda is ~1-2 orders of magnitude faster than sander and pmemd is ~2x faster with better parallel scaling).
Long story short, I don't think this question has been thoroughly investigated (if investigated at all). If I had to guess which one would be better, I'd probably still pick TIP4Pew (it gives better properties under a more theoretically rigorous treatment of long-range electrostatics). But it's really just my intuition applied to a model that I never use, so take that for what it's worth.
HTH,
Jason
P.S. My expectation is, actually, that it would make no discernible difference, and the effect of TIP4P vs. TIP4Pew would be tiny compared to the effect of the solvent cap.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jul 27 2015 - 07:30:02 PDT
