Hi Anamika,
if you use Particle-Mesh-Ewald (PME) electrostatics these parameters
are used to control the (discrete) grid layout onto which the electrostatic
charges are extrapolated (from their continuous positions).
The basic value of 0.12 nm for the fourierspacing means that you will have
a PME grid point at least every 0.12 nm in x, y, and z direction. The number of
PME
grid points in each direction is then calculated by grompp satisfying the
fourierspacing condition. grompp then also outputs how many grid points are
actually used, e.g.
Using a fourier grid of 30x30x30, spacing 0.118 0.118 0.118
Together with the value of the pme_order parameter, which defaults to 4, the
accuracy of the calculation of the long-range part is set. A higher pme_order
and a smaller fourierspacing (more grid points) result in a more accurate
(and time-consuming) calculation.
You might want to read one of the following papers for a deeper understanding
of the PME parameters:
Markus Deserno and Christian Holm. How to mesh up Ewald sums I. A theoretical
and numerical comparison of various particle mesh routines. J. Chem. Phys.,
109:7678, 1998.
Ulrich Essmann, Lalith Perera, Max L. Berkowitz, Tom Darden, Hsing Lee, Lee G.
Pedersen,
A smooth Particle Mesh Ewald method, J. Chem. Phys., 1995, vol. 103, 19, pages
8577-8593
Hope that helps,
Carsten
Anamika Awasthi wrote:
Dear Gromacs user,
Please tell me what is the significance of fourier grid and spacing in
MD simulation?
Thanks in advance
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/research/dep/grubmueller/
http://www.gwdg.de/~ckutzne
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