On Mon, Aug 9, 2010 at 9:58 AM, <poj...@icp.uni-stuttgart.de> wrote: > Hi, > > I want to use the pme algorithm in GROMACS. Thge size of my box is > 8.2x8.2x8.2 in reduced units. I am considering a collection of 1000 > of CO2 molecules. If I am using reduced units, the values of the > parameters "rcoulomb=0.9" I think should be converted to reduced > units "rcoulomb=2.45" (my \sigma=0.366nm). But my question is how > can one convert the value of "fourierspacing=0.12" to reduced units? >
'fourierspacing' is also in units of length and it's value is used to determine 'fourier_nx' etc., if the latter are set to zero. In that case, fourier_nx=(box length along x)/fourierspacing. So for same level of PME accuracy scale down 'fourierspacing' by sigma=0.366 also. > > > > > (This script is in SI standard units) > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = pme > rcoulomb-switch = 0 > rcoulomb = 0.9 > ; Dielectric constant (DC) for cut-off or DC of reaction field > epsilon-r = 1 > ; Method for doing Van der Waals > vdw-type = Cut-off > ; cut-off lengths > rvdw-switch = 0 > rvdw = 0.9 > ; Apply long range dispersion corrections for Energy and Pressure > DispCorr = EnerPres > ; Extension of the potential lookup tables beyond the cut-off > table-extension = 1 > ; Spacing for the PME/PPPM FFT grid > fourierspacing = 0.12 > ; FFT grid size, when a value is 0 fourierspacing will be used > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > ; EWALD/PME/PPPM parameters > pme_order = 4 > ewald_rtol = 1e-05 > ewald_geometry = 3d > epsilon_surface = 0 > optimize_fft = no > > > Thanks. > > -- > 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/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/mailing_lists/users.php >
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