[gmx-users] User-defined potentials and meaning of table extension
dmer018 at aucklanduni.ac.nz
Fri Mar 21 10:22:25 CET 2014
Hello GMX users,
I am testing the use of User-defined on a box of water and I came across
the issue of table-extension option.
I don't understand the use of it. If I specify a cutoff of 1 nm and then
give a table extension of 0 nm then the cutoff will be 1 nm otherwise it
will be cutoff+table-extension value. This is pretty clear. However, it is
not clear why a table extension is needed.
As a test, I have run this on only two water molecules placed at a distance
within the cutoff coupled to table-extension = 0nm and to table-extension =
In both cases, the values listed in the table seem to be considered up to
the cut-off and the table extension seem to be ignored?
A puzzling thing that happened is that then, for a box of water (216
molecules), using table extension = 0 nm (cutoff 0.5 nm) I get an unstable
and crashing simulation, while if I use table extension = 1 nm (cutoff 0.5
nm) the system runs smoothly.
Can you please help me to understand this?
Any comments will be very much appreciated.
Thank you in advance for your time.
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