BUG? reinitatoms on wrapped coordinates occasionally fail with rigidbonds

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Mar 13 2019 - 03:05:56 CDT

Hey there,


I came across some weird behavior with some special use of the reinitatoms
command. The coordinates I'm reading are wrapped by PBC, a receptor is
centered in the box and so a ligand residue is sometimes broken across PBC.
However, along with the correct box

dimensions read from xsc file, this shouldn't be a problem for NAMD right?
Unfortunately it is. The structures I'm triying to read are definitely
correctly wrapped, but sometimes, NAMD seems to wrongly threat the broken
residues when dividing the patches and this is correlated to rigidbonds.

With rigidbonds enabled, broken residues are occasionally distorted but not
when having "rigidbonds none", where everything works as expected.


I report this hoping, that a respective NAMD developer will have a clue
where this problem might come from.


Best wishes

Norman Geist

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