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 <jalem...@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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists