On 3/12/18 3:42 PM, Alex wrote:
I actually understood your tutorial perfectly well. What I didn't
expect is such a significant dependence on direction (assuming
spherical symmetry clears the situation).
I also had to use direction-periodic instead of distance in your
tutorial, because the box is 4 nm wide and grompp is screaming about
distance exceeding half-box size. I used 5.0.3 before and it was fine
with the 'distance' directive. I think 'direction-periodic' is also
wrong for spherical symmetry. So, stick with distance and increase box
size?
That's the easiest thing to do, yes, as long as the simulation is still
reasonably efficient.
-Justin
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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
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