From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Mar 13 2019 - 13:43:16 CDT
I assume the coordinates were wrapped per-atom by some tool.
NAMD is probably expecting hydrogen coordinates to be in the same image as
their bonded heavy atom. The bonded energy code wraps coordinates but the
rigid bond code may be making some assumption.
Jim
On Wed, 13 Mar 2019, Norman Geist wrote:
> 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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