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 [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
