[gmx-users] Reduced Units

[Gaurav Goel]

On Mon, Aug 9, 2010 at 9:58 AM, <pojeda at 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.
>
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