Re: [gmx-users] Long range Lennard Jones
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)
Re: [gmx-users] Long range Lennard Jones
On 8/29/13 6:23 PM, Gianluca Interlandi wrote: And interestingly, they point out at differences between the various implementations of the switching function. Also, when trying to replicate the CHARMM energies, the authors did not use any cutoff at all and performed the calculations in vacuo. If you look at Table 1 in the paper, it is exactly LJ where the most discrepancies are, i.e., 0.008 kJ/Mol for homeopeptides consisting of 4 AA. I copy the text here (lower left corner of page 3, first paragraph of Results): For testing the correctness of the force field implementation, we compared the values for the potential energy of all amino acids to the force field included in the c33b1 release of CHARMM and NAMD version 2.7b2 (Table 1). The CMAP implementation was also validated by comparing forces. These calculations were performed in vacuo without cutoffs, since implementation detail differences between CHARMM and GROMACS make it difficult to get exactly identical results with other setup schemes. For example, CHARMM does not necessarily work with charge groups, switch/shift functions are not the same, and deinitions of interaction cutoffs differ as well as rules for neighbor searching. Yes, this is typical for comparing energies between software packages. It would have been interesting if they had done the comparions using the recommended 10/12/14 cutoff (although PME would have been compulsory since gromacs Shift function completely differs from CHARMM SHIFT). They did, later in the protein simulations. It seems that they achieved the expected behavior, though probably other demonstrations could still be done. In any case, it would be very easy to draw up a simple system of some standard compound in water and calculate energies using both Gromacs and CHARMM using the equivalent (switch/shift differences aside) setups. -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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
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 listgmx-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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
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? I have tested only full proteins over a 50-ns period. I have not calculated yet the water interaction energies. Do you mean by that just the force field interaction energy bulk-bulk? I plan to test how much it affects FEP calculations. 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. I mean, performance is a factor to consider when accuracy is not affected. I don't recall what the reviewer's reasoning was. They probably did their recommendation in good faith that it won't affect accuracy. But I agree that one should test how much the system is affected. Gianluca - 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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
On 8/29/13 2:52 PM, Gianluca Interlandi wrote: 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? I have tested only full proteins over a 50-ns period. I have not calculated yet the water interaction energies. Do you mean by that just the force field interaction energy bulk-bulk? I plan to test how much it affects FEP calculations. I'm thinking more along the lines of the underlying CHARMM parameterization - MM water interaction energies between model compounds and whether or not the new cutoffs recapitulate the original CHARMM MM energies with the standard values. 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. I mean, performance is a factor to consider when accuracy is not affected. I don't recall what the reviewer's reasoning was. They probably did their recommendation in good faith that it won't affect accuracy. But I agree that one should test how much the system is affected. Of course, if accuracy is not in question then performance dominates. I have seen countless reports on this list and elsewhere where small changes in cutoffs lead to wildly incorrect behavior, affecting every force field. Thus, I am always extremely skeptical of such changes. The effects can be subtle but non-negligible. -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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
Of course, if accuracy is not in question then performance dominates. I have seen countless reports on this list and elsewhere where small changes in cutoffs lead to wildly incorrect behavior, affecting every force field. Thus, I am always extremely skeptical of such changes. The effects can be subtle but non-negligible. I would be very interested in reading about some of these reports. I have searched the gromacs forum and I have found similar discussions but never accompanied by actual benchmarks with numbers, or maybe I have not searched carefully enough! Gianluca == 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 listgmx-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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
On 8/29/13 5:15 PM, Gianluca Interlandi wrote: Of course, if accuracy is not in question then performance dominates. I have seen countless reports on this list and elsewhere where small changes in cutoffs lead to wildly incorrect behavior, affecting every force field. Thus, I am always extremely skeptical of such changes. The effects can be subtle but non-negligible. I would be very interested in reading about some of these reports. I have searched the gromacs forum and I have found similar discussions but never accompanied by actual benchmarks with numbers, or maybe I have not searched carefully enough! They tend to show up in reports of crashes, structures falling apart, and failure to reproduce membrane properties (which is extremely sensitive to cutoff values). One such example that I recall having occurred recently: http://lists.gromacs.org/pipermail/gmx-users/2013-January/078269.html Previous posts in that thread have lots of information. -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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
And also, gromacs does not seem to use the same switching function as CHARMM. Has it been tested how much this affects replication of the original CHARMM MM energies? Gianluca On Thu, 29 Aug 2013, Gianluca Interlandi wrote: Of course, if accuracy is not in question then performance dominates. I have seen countless reports on this list and elsewhere where small changes in cutoffs lead to wildly incorrect behavior, affecting every force field. Thus, I am always extremely skeptical of such changes. The effects can be subtle but non-negligible. I would be very interested in reading about some of these reports. I have searched the gromacs forum and I have found similar discussions but never accompanied by actual benchmarks with numbers, or maybe I have not searched carefully enough! Gianluca == 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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
On 8/29/13 5:33 PM, Gianluca Interlandi wrote: And also, gromacs does not seem to use the same switching function as CHARMM. Has it been tested how much this affects replication of the original CHARMM MM energies? Yes. dx.doi.org/10.1021/ct900549r -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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
Yes, I've seen that thread before. My feeling is that simulating membranes with the CHARMM36 FF is a different story. It's good to be aware of that. Gianluca On Thu, 29 Aug 2013, Justin Lemkul wrote: On 8/29/13 5:15 PM, Gianluca Interlandi wrote: Of course, if accuracy is not in question then performance dominates. I have seen countless reports on this list and elsewhere where small changes in cutoffs lead to wildly incorrect behavior, affecting every force field. Thus, I am always extremely skeptical of such changes. The effects can be subtle but non-negligible. I would be very interested in reading about some of these reports. I have searched the gromacs forum and I have found similar discussions but never accompanied by actual benchmarks with numbers, or maybe I have not searched carefully enough! They tend to show up in reports of crashes, structures falling apart, and failure to reproduce membrane properties (which is extremely sensitive to cutoff values). One such example that I recall having occurred recently: http://lists.gromacs.org/pipermail/gmx-users/2013-January/078269.html Previous posts in that thread have lots of information. -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 listgmx-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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
And interestingly, they point out at differences between the various implementations of the switching function. Also, when trying to replicate the CHARMM energies, the authors did not use any cutoff at all and performed the calculations in vacuo. If you look at Table 1 in the paper, it is exactly LJ where the most discrepancies are, i.e., 0.008 kJ/Mol for homeopeptides consisting of 4 AA. I copy the text here (lower left corner of page 3, first paragraph of Results): For testing the correctness of the force field implementation, we compared the values for the potential energy of all amino acids to the force field included in the c33b1 release of CHARMM and NAMD version 2.7b2 (Table 1). The CMAP implementation was also validated by comparing forces. These calculations were performed in vacuo without cutoffs, since implementation detail differences between CHARMM and GROMACS make it difficult to get exactly identical results with other setup schemes. For example, CHARMM does not necessarily work with charge groups, switch/shift functions are not the same, and deinitions of interaction cutoffs differ as well as rules for neighbor searching. It would have been interesting if they had done the comparions using the recommended 10/12/14 cutoff (although PME would have been compulsory since gromacs Shift function completely differs from CHARMM SHIFT). Gianluca On Thu, 29 Aug 2013, Justin Lemkul wrote: On 8/29/13 5:33 PM, Gianluca Interlandi wrote: And also, gromacs does not seem to use the same switching function as CHARMM. Has it been tested how much this affects replication of the original CHARMM MM energies? Yes. dx.doi.org/10.1021/ct900549r -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 listgmx-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 listgmx-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] Long range Lennard Jones
Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca - 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 listgmx-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
RE: [gmx-users] Long range Lennard Jones
DispCorr might be what you are looking for, correction for LJ beyond the cut-off. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Gianluca Interlandi Sent: Wednesday, 28 August 2013 4:36 PM To: gmx-users@gromacs.org Subject: [gmx-users] Long range Lennard Jones Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca - 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 listgmx-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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
Lennard-Jones PME is planned for 5.0 Mark On Aug 28, 2013 8:36 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca --**--- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.**washington.edu/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 listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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
Re: [gmx-users] Long range Lennard Jones
Hi, What is LJ PME? I googled it and got this publication? http://pubs.acs.org/doi/abs/10.1021/ct400146w So, LJ will not be cut off at some r, but you will have a real+fourier part similar to electrostatics. Is that LJ PME? What are the advantages? On Wed, Aug 28, 2013 at 12:36 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Lennard-Jones PME is planned for 5.0 Mark On Aug 28, 2013 8:36 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca --**--- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.**washington.edu/ 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 listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-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
Re: [gmx-users] Long range Lennard Jones
On 2013-08-28 09:31, rajat desikan wrote: Hi, What is LJ PME? I googled it and got this publication? http://pubs.acs.org/doi/abs/10.1021/ct400146w So, LJ will not be cut off at some r, but you will have a real+fourier part similar to electrostatics. Is that LJ PME? What are the advantages? http://pubs.acs.org/doi/abs/10.1021/ct400140n On Wed, Aug 28, 2013 at 12:36 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Lennard-Jones PME is planned for 5.0 Mark On Aug 28, 2013 8:36 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca --**--- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.**washington.edu/ 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 listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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
Re: [gmx-users] Long range Lennard Jones
Secondarily, one could use the same cut-off for LJ and electrostatics, and treat their respective lattice components however you like. This simplifies implementations for computing short-ranged interactions, while facilitating iso-accuracy load balancing across heterogeneous compute units. Mark On Wed, Aug 28, 2013 at 10:08 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2013-08-28 09:31, rajat desikan wrote: Hi, What is LJ PME? I googled it and got this publication? http://pubs.acs.org/doi/abs/10.1021/ct400146w So, LJ will not be cut off at some r, but you will have a real+fourier part similar to electrostatics. Is that LJ PME? What are the advantages? http://pubs.acs.org/doi/abs/10.1021/ct400140n On Wed, Aug 28, 2013 at 12:36 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Lennard-Jones PME is planned for 5.0 Mark On Aug 28, 2013 8:36 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca --**--- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.**washington.edu/ 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 listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
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. Gianluca On Wed, 28 Aug 2013, Mark Abraham wrote: Secondarily, one could use the same cut-off for LJ and electrostatics, and treat their respective lattice components however you like. This simplifies implementations for computing short-ranged interactions, while facilitating iso-accuracy load balancing across heterogeneous compute units. Mark On Wed, Aug 28, 2013 at 10:08 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2013-08-28 09:31, rajat desikan wrote: Hi, What is LJ PME? I googled it and got this publication? http://pubs.acs.org/doi/abs/10.1021/ct400146w So, LJ will not be cut off at some r, but you will have a real+fourier part similar to electrostatics. Is that LJ PME? What are the advantages? http://pubs.acs.org/doi/abs/10.1021/ct400140n On Wed, Aug 28, 2013 at 12:36 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Lennard-Jones PME is planned for 5.0 Mark On Aug 28, 2013 8:36 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca --**--- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.**washington.edu/ 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 listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
Current CHARMM development relies on a 1.2-nm cutoff for LJ, so that's how we balance all of the forces during parameterization. Ok, I agree. What about the use of PME for Coulomb? The CHARMM PARAM22 force field was parametrized using SHIFT on electrostatic forces making it zero after 12 A (please note that SHIFT and FSHIFT in CHARMM greatly differ from the gromacs-style Shift). Also, the CHARMM switch function is different from gromacs Switch (at least from what I can tell reading pages 71-72 of the gromacs manual 4.6.3). Thanks, Gianluca 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 listgmx-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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
On 8/28/13 9:09 PM, Gianluca Interlandi wrote: Current CHARMM development relies on a 1.2-nm cutoff for LJ, so that's how we balance all of the forces during parameterization. Ok, I agree. What about the use of PME for Coulomb? The CHARMM PARAM22 force field was parametrized using SHIFT on electrostatic forces making it zero after 12 A (please note that SHIFT and FSHIFT in CHARMM greatly differ from the gromacs-style Shift). Also, the CHARMM switch function is different from gromacs Switch (at least from what I can tell reading pages 71-72 of the gromacs manual 4.6.3). PME is generally vastly better than switched or shifted electrostatics. This has been demonstrated in the literature consistently over many years. -Justin Thanks, Gianluca 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 listgmx-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 - -- == 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 listgmx-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
Re: [gmx-users] Long range Lennard Jones
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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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 listgmx-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
