PBC BUG in coorfile + pair interaction

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jan 21 2016 - 03:50:59 CST

Hey there,


seems I've encountered a bug in how namd handles the missing pairlists when
using the coorfile command to read in frames from a dcd trajectory
(basically by using VMDs NAMD Energy plugin). It looks like NAMD doesn't
consider the periodic boundary condition to find out which atoms are in
interaction distance. This can be seen by trying to compute pair interaction
energies for two selection that do only meet across the periodic boundaries.
One will get only zeros for all energies, which will only change by choosing
high cutoff values like 100A.


Best wishes


Norman Geist


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