Justin,
I respect your opinion on this. However, in the paper indicated below by
BR Brooks they used a cutoff of 10 A on LJ when testing IPS in CHARMM:
Title: Pressure-based long-range correction for Lennard-Jones interactions
in molecular dynamics simulations: Application to alkanes and interfaces
Author(s): Lague, P; Pastor, RW; Brooks, BR
Source: JOURNAL OF PHYSICAL CHEMISTRY B Volume: 108 Issue: 1 Pages:
363-368 Published: JAN 8 2004
There is also a paper by Piana and Shaw where different cutoffs for
non-bonded are tested with CHARMM22 on Anton:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039918
They found some subtle differences, in particular for cutoffs shorter than
9 A. However, Anton uses abrupt truncation (no switching) and I believe
that the differences they found at cutoffs > 9 A would be much smaller if
they had used a finer mesh (as they show at the 8 A cutoff). I always use
fourierspacing=1.0
I agree though that it strongly depends on the system and I have always
run control simulations but never found significant differences in the
case of just proteins.
Finally, I have not tested it in gromacs, but in NAMD there is a
performance gain of 25% when using the shorter cutoff. This is a factor to
consider. When I asked for Teragrid supercomputing allocations back in
2006 and 2007 and I suggested 10/12/14 cutoff, the reviewers always
complained and cut my requested time of 20% with the justification that I
must use a shorter cutoff.
Gianluca
On Wed, 28 Aug 2013, Justin Lemkul wrote:
On 8/28/13 7:28 PM, Gianluca Interlandi wrote:
Thanks for your replies, Mark. What do you think about the current DispCorr
option in gromacs? Is it worth it trying it? Also, I wonder whether using
DispCorr for LJ + PME for Cb justifies reducing the cutoff for non-bonded
to 1
nm with the CHARMM force field, where 1.2 nm is usually recommended.
This is risky. Current CHARMM development relies on a 1.2-nm cutoff for LJ,
so that's how we balance all of the forces during parameterization. To me,
ad hoc changes like these are not worth the tiny (potential) increase in
performance. As I recently told someone else on this topic, if you're intent
on fiddling with the typical workings of a force field, especially if you're
making changes to something so fundamental, be prepared to undertake a
demonstration that you can recapitulate all of the expected outcomes of the
force field or improve upon them. My gut feeling, in this case and others,
is that you won't be able to. You're messing with something that is fairly
critical to obtaining sensible results.
As for dispersion correction, it is generally helpful, but it assumes a
homogeneous environment. If you simulate with a membrane, for instance, this
assumption breaks down, though some literature suggests that use of
dispersion correction in these cases is still better than nothing.
-Justin
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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Baltimore, MD 21201
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