AW: PBC BUG in coorfile + pair interaction

From: Norman Geist (
Date: Thu Jan 21 2016 - 04:32:33 CST

It could also be related to the fact, that VMDs NAMD Energy Plugin generates
a NAMD input that doesn't contain CellBasisVector statements. So NAMD
performs its domain decomposition before having the right box information.
Anyway, when actually having the box after using "coorfile read", NAMD
shouldn't fail to include all interactions within cutoff, or?


Norman Geist


Von: [] Im Auftrag
von Norman Geist
Gesendet: Donnerstag, 21. Januar 2016 10:51
Betreff: namd-l: PBC BUG in coorfile + pair interaction


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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