[gmx-users] table-extension distance appears to be over-ridden by .mdp file cut-off values

ploetz ploetz at ksu.edu
Thu Dec 19 02:43:59 CET 2013

Hi again,

I forgot to mention that when I did the test of moving the single water
molecule around in the presence of the LJ-sphere, I set the water charges to
zero, so it was only a test of the VdW interactions. Also, I removed the HW
atoms, since they have sigma=epsilon=0. So the test system was really just a
LJ-sphere and an OW atom, with the OW atom being moved around to different
distances away from the LJ-sphere in an attempt to map out the VdW potential

Furthermore, I just repeated that test using a different tabulated
potential. I used a Lennard Jones 2-3 (just playing around):
(I just wanted to try something very different from the 6-12 potential so I
would know if the table was being used up to 0.8 nm or just being ignored.)
The plot below shows that the table is being used, but the table-extension
.mdp option does not seem to be being used. For all sphere - OW distances
>=0.8 nm, the LJ(SR) energy was zero (those points were not plotted).




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