On Mon, Aug 9, 2010 at 9:58 AM, <span dir="ltr"><<a href="mailto:pojeda@icp.uni-stuttgart.de">pojeda@icp.uni-stuttgart.de</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
I want to use the pme algorithm in GROMACS. Thge size of my box is<br>
8.2x8.2x8.2 in reduced units. I am considering a collection of 1000<br>
of CO2 molecules. If I am using reduced units, the values of the<br>
parameters "rcoulomb=0.9" I think should be converted to reduced<br>
units "rcoulomb=2.45" (my \sigma=0.366nm). But my question is how<br>
can one convert the value of "fourierspacing=0.12" to reduced units?<br></blockquote><div><br>'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. <br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
<br>
<br>
(This script is in SI standard units)<br>
; OPTIONS FOR ELECTROSTATICS AND VDW<br>
; Method for doing electrostatics<br>
coulombtype = pme<br>
rcoulomb-switch = 0<br>
rcoulomb = 0.9<br>
; Dielectric constant (DC) for cut-off or DC of reaction field<br>
epsilon-r = 1<br>
; Method for doing Van der Waals<br>
vdw-type = Cut-off<br>
; cut-off lengths<br>
rvdw-switch = 0<br>
rvdw = 0.9<br>
; Apply long range dispersion corrections for Energy and Pressure<br>
DispCorr = EnerPres<br>
; Extension of the potential lookup tables beyond the cut-off<br>
table-extension = 1<br>
; Spacing for the PME/PPPM FFT grid<br>
fourierspacing = 0.12<br>
; FFT grid size, when a value is 0 fourierspacing will be used<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
; EWALD/PME/PPPM parameters<br>
pme_order = 4<br>
ewald_rtol = 1e-05<br>
ewald_geometry = 3d<br>
epsilon_surface = 0<br>
optimize_fft = no<br>
<br>
<br>
Thanks.<br>
<font color="#888888"><br>
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