[gmx-users] Long range Lennard Jones

[Michael Shirts]

IPS in CHARMM involves additional calculations beyond a simple
homogeneous approximation -- roughly equivalent to PME for dispersion,
though its a bit messier.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723858/



On Thu, Aug 29, 2013 at 7:56 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 8/29/13 1:18 AM, Gianluca Interlandi wrote:
>>
>> 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
>>
>
> I cannot say for sure whether the DispCorr implementation in Gromacs is the
> same or comparable to IPS in CHARMM.  You would have to test that, and also
> test a more complex system than simple liquids.
>
>
>> 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
>>
>
> Note that Shaw's group is using their own modified force field, CHARMM22*,
> so that factors in here, as well.  I do recall that paper, though I haven't
> read it in a while, so details may be fuzzy.  Wasn't the principal point to
> test methods for long-range electrostatics and the influence of cutoffs in
> that context?  I seem to recall LJ taking a backseat there.  It is certainly
> true that short-range Coulomb cutoffs are more flexible when using Ewald
> methods.
>
>
>> 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.
>>
>
> That's good to know that you've tested different setups.  Are the water
> interaction energies comparable?  Have you tested model compounds or just
> full proteins?  Over how long of a time period?
>
>
>> 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.
>>
>
> That's unfortunate.  In my opinion, it is shameful that desired performance
> exceeds proven integrity of the data.  If all we're after is performance, I
> can write up a dozen papers in the next few months with completely useless
> data, but they will be produced quickly! ;)
>
>
> -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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