On Thu, Aug 29, 2013 at 7:18 AM, Gianluca Interlandi <gianl...@u.washington.edu> 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 > > 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.
I'm not sure about what "the sorter cutoff" refers to, neither about the context Let me pitch in with little bit of clarification on computational costs, I hope somebody can make use of it. Note that I don't want to argue for the use of shorter cut-offs - although revising a "magic simulation recipe" one used just because that's what one was provided may be advantageous anyway. The performance gain from a shorter cut-off depends on several factors (and most of these factors are _not_ GROMACS-specific): 1) Performance of the short-range and (vs) long-range interaction algorithm/implementation; 2) Scaling of short-range and long-range parts of the code (a given implementation on a given hardware, note that not all implementations are equal!); 3) If some sort of task-parallelization is used, e.g. accelerator offloading (GPUs) or "PME nodes" in GROMACS, depending on the implementation, a longer cut-off can sometimes be free lunch or it can even improve performance. For instance, with GROMACS 4.6 if you have a very fast GPU (wrt the CPU) you may get the same or better performance with a longer cut-off. 4) Single or twin cut-off (rcoul = rvdw?). (+probably a few more that I forgot about :) Given the fact that e.g. a 1.2 nm cut-off will result in a 1.73x larger interaction volume than 1.0 nm, this will obviously drive up the cost of short-range interactions. Hence, in this case, 1 nm cut-off will in most cases give faster simulations. As mentioned above, exception can be cases when, due to imbalanced PP-PME load, reducing the PME cost is advantageous e.g. fast GPU case or at high parallelization. -- Szilárd > 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 >> >> 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 >> > > ----------------------------------------------------- > Gianluca Interlandi, PhD gianl...@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 > ----------------------------------------------------- > -- > 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