Hi, On Wed, 18 Mar 2020 at 07:02, Anh Vo <at...@msstate.edu> wrote:
> Hi everyone, > > I'm trying to reconstruct in GROMACS some LAMMPS simulation to compare > between the two. I'm simulating a lipid bilayer system with 72 POPC lipids > and 9072 water molecules, as well as a single lipid system (1 POPC > molecule) and water only system (100 H2O molecules). > Start with a simpler system when proving you understand how to set up equivalent simulations. I try to use the same settings in GROMACS as in LAMMPS. However, in LAMMPS > I have *kspace_style* to define a long-range solver and *kspace_modify* to > set > parameters used by the kspace solvers; but I'm not sure which command I > should use for similar settings in GROMACS. (I have read the manual and > searched online but haven't figured it out. Please accept my apology if > this seems to be an obvious question). > > In details, these 2 commands in LAMMPS are: > * - kspace_style pppm 1e-5 *(pppm is P3M algorithm, 1.0e-5 means > that the RMS error will be a factor of 100,000 smaller than the reference > force) > Then you'll know that ewald_rtol does exactly that, and that http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-value-coulombtype=P3M-AD does what you want. * - kspace_modify diff ad *(*diff* keyword specifies the > differentiation scheme used by the PPPM method to compute forces on > particles, *ad* keyword means approach uses only 1 FFT to transfer > information back to real space for a total of 2 FFTs per timestep). > > Please help me to get similar settings in GROMACS (e.g. which command > should I use ?). Also, would it make a significant difference (e.g. in the > energy of the molecules, in the output pressure, etc.) if I use PME instead > of PPPM in GROMACS ? > No need to do that. Mark > Thank you very much for your help. > > Best, > Anh Vo > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
