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 <mark.j.abra...@gmail.com>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 <fdusuperstr...@gmail.com> 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 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