AW: Weird PBC wrapping

From: Norman Geist (
Date: Fri Aug 31 2018 - 01:58:11 CDT

Yes, you probably want –compound fragment?


Von: [] Im Auftrag von Giacomo Fiorin
Gesendet: Donnerstag, 30. August 2018 15:42
An: NAMD list <>;
Betreff: Re: namd-l: Weird PBC wrapping


The -compound residue may be the cause. Please check the meaning of -compound, and adjust it accordingly:


On Thu, Aug 30, 2018 at 6:42 AM Michail Lazaratos < <> > wrote:

Dear NAMD users,

i observed weird water behavior when PBC wrapping my system
(protein,membrane & water).

I have attached 2 sample mpg files. Hope it is not too long.

The command i used is:
pbc wrap -centersel "protein" -center com -compound residue -all

Do you have any suggestions? Is my wrapping command wrong to begin with?

Thank you in advance,

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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