[gmx-users] Long range Lennard Jones
gianluca at u.washington.edu
Thu Aug 29 07:18:15 CEST 2013
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:
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
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.
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 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
> gmx-users mailing list gmx-users at gromacs.org
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Gianluca Interlandi, PhD gianluca at u.washington.edu
+1 (206) 685 4435
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
More information about the gromacs.org_gmx-users