Re: [gmx-users] The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme
If one is using the potential for something (e.g. reweighting, replica exchange) then now the possibility of a systematic deviation with shifted potentials is real. Mark On Thu, May 23, 2013 at 10:11 PM, Mark Abraham wrote: > Those modifiers shift only the potential, as manual 7.3 points out. So the > forces and sampling are unaffected, so it does not surprise me that APL is > unaffected by the use of such a shift. If your group cutoff scheme was > unbuffered (rlist <= max(rcoulcomb,rvdw) and nstlist > 1), then if the > observed difference is significant, then that could be the reason. > > Mark > > > > On Thu, May 23, 2013 at 9:44 PM, Bin Liu wrote: > >> Hi All, >> >> In GROMACS 4.6.x series, Verlet cutoff scheme is introduced to enable >> OpenMP parallelization and GPU acceleration. Then some new run parameters >> are introduced to control the use of Verlet cutoff scheme. However, I >> noticed the GROMACS manual doesn't give in-depth knowledge on some >> parameters. For example, I am sure whether and how to use >> the coulomb-modifier and vdw-modifier parameters with Verlet cutoff >> scheme. >> My shallow experience told me these two parameters won't affect the >> simulation much in term of speed and accuracy. I did a rough benchmark on >> a >> DMPC128 bilayer (323K) system to check the area per lipid against >> (traditional) group cutoff scheme results. >> >> Group cutoff scheme: 0.656 (0.008) nm^2 (Uncertainty) >> >> Verlet cutoff scheme (rcoulomb=rvdw=1.0, coulomb-modifier = >> Potential-shift-Verlet, vdw-modifier = Potential-shift-Verlet) 0.643nm^2 >> >> Verlet cutoff scheme (rcoulomb=rvdw=1.0, coulomb-modifier = None, >> vdw-modifier = None) 0.645nm^2 >> >> Basically the results from two Verlet cutoff parameter sets are >> indistinguishable. I am looking forward to your help to give me some >> insight into this question. >> >> Thank you very much. >> >> Regards >> >> Bin >> -- >> 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] The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme
Those modifiers shift only the potential, as manual 7.3 points out. So the forces and sampling are unaffected, so it does not surprise me that APL is unaffected by the use of such a shift. If your group cutoff scheme was unbuffered (rlist <= max(rcoulcomb,rvdw) and nstlist > 1), then if the observed difference is significant, then that could be the reason. Mark On Thu, May 23, 2013 at 9:44 PM, Bin Liu wrote: > Hi All, > > In GROMACS 4.6.x series, Verlet cutoff scheme is introduced to enable > OpenMP parallelization and GPU acceleration. Then some new run parameters > are introduced to control the use of Verlet cutoff scheme. However, I > noticed the GROMACS manual doesn't give in-depth knowledge on some > parameters. For example, I am sure whether and how to use > the coulomb-modifier and vdw-modifier parameters with Verlet cutoff scheme. > My shallow experience told me these two parameters won't affect the > simulation much in term of speed and accuracy. I did a rough benchmark on a > DMPC128 bilayer (323K) system to check the area per lipid against > (traditional) group cutoff scheme results. > > Group cutoff scheme: 0.656 (0.008) nm^2 (Uncertainty) > > Verlet cutoff scheme (rcoulomb=rvdw=1.0, coulomb-modifier = > Potential-shift-Verlet, vdw-modifier = Potential-shift-Verlet) 0.643nm^2 > > Verlet cutoff scheme (rcoulomb=rvdw=1.0, coulomb-modifier = None, > vdw-modifier = None) 0.645nm^2 > > Basically the results from two Verlet cutoff parameter sets are > indistinguishable. I am looking forward to your help to give me some > insight into this question. > > Thank you very much. > > Regards > > Bin > -- > 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
[gmx-users] The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme
Hi All, In GROMACS 4.6.x series, Verlet cutoff scheme is introduced to enable OpenMP parallelization and GPU acceleration. Then some new run parameters are introduced to control the use of Verlet cutoff scheme. However, I noticed the GROMACS manual doesn't give in-depth knowledge on some parameters. For example, I am sure whether and how to use the coulomb-modifier and vdw-modifier parameters with Verlet cutoff scheme. My shallow experience told me these two parameters won't affect the simulation much in term of speed and accuracy. I did a rough benchmark on a DMPC128 bilayer (323K) system to check the area per lipid against (traditional) group cutoff scheme results. Group cutoff scheme: 0.656 (0.008) nm^2 (Uncertainty) Verlet cutoff scheme (rcoulomb=rvdw=1.0, coulomb-modifier = Potential-shift-Verlet, vdw-modifier = Potential-shift-Verlet) 0.643nm^2 Verlet cutoff scheme (rcoulomb=rvdw=1.0, coulomb-modifier = None, vdw-modifier = None) 0.645nm^2 Basically the results from two Verlet cutoff parameter sets are indistinguishable. I am looking forward to your help to give me some insight into this question. Thank you very much. Regards Bin -- 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
