On 11/6/13 4:52 PM, Mark Abraham wrote:
On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/6/13 2:14 PM, Ehsan Sadeghi wrote:
Many thanks Justin. What is an appropriate cut-off value? My box size is
d=
0.5 nm; based on the definition of cut-off radius, its value shouble be
smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I
right?
No. The cutoff value is not a function of box size; it is a fixed
property of the force field. No wonder the simulation is crashing. If
your box is only 0.5 nm, then a cutoff of 1.5 nm is triple-counting
interactions across PBC!
Triple counting is not possible, per minimum-image convention. I think
True. Thinking too quickly ;)
Ehsan's report of a "0.5nm" box size is probably wrong, e.g. per its
documentation, editconf -d 0.5 does not produce a 0.5nm box.
editconf -box 0.5 does produce such a box, though, so it is possible. grompp
should have warned quite obviously about the combination of a 0.5-nm box with
1.5-nm cutoffs, though.
-Justin
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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