[gmx-users] Long range Lennard Jones

[Gianluca Interlandi]

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
>
> -- 
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
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-----------------------------------------------------
Gianluca Interlandi, PhD gianluca at u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
                     http://healthynaturalbaby.org
-----------------------------------------------------