From: da xue (adderxue_at_gmail.com)
Date: Tue Mar 29 2011 - 20:28:26 CDT
Dear NAMD developers and users,
Recently, I run a NPT ensemble for the glycerol solution by NAMD. The
initial simulation box is definitely not at equilibrium and the distances
between molecules are man-made large. So, after several steps, the
simulation box will shrink obviously to achieve a reasonable distribution of
molecules.
In the Configuration file, I set the GridSizeX, Y and Z according to the
used's guide without setting the PMEGridSpacing. For example,
cellBasicVector1 31 0 0
cellBasicVector2 0 44 0
cellBasicVector3 0 0 51
cellOrigin 0 0 0
PMEGridSizeX 32
PMEGridSizeY 45
PMEGridSizeZ 54
*My questions are below.*
1. What value will the PMEGridSpacing hold if I set the above PMEGridSizeX,
Y and Z?
2. Considering the obvious shrink of the initial simulaiton box, will the
PMEGridSizeX, Y and Z (set according to the initial size of the box) be
effective throughout the simulation period? How do I set PMEGridSizeX, Y and
Z when the initial simulation box is larger than the equilibirium box
obviously?
3. How are PMEGridSizeX, Y and Z and PMEGridSpacing converted to each other?
4. I imagine. It is the PMEGridSpacing that takes effect throughout the
simulation period. The initially-set PMEGridSizeX, Y and Z can only be used
to calculate the PMEGridSpacing and they will be negelected when
PMEGridSpacing is calculated?
5. What does *PME direct space tolerance* really mean? I found several
different ways to express it. For example, "with a direct sum tolerance of
10E-6 at the 9 A direct space cutoff" or "with a direct space sum tolerance"
.. Which one is more proper?
With kind regards.
Lindong Weng
Dalian University of Technology
Dalian, Liaoning Prov., P.R.China
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