AW: Weird PBC wrapping

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Aug 31 2018 - 01:58:11 CDT

Yes, you probably want –compound fragment?

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Giacomo Fiorin
Gesendet: Donnerstag, 30. August 2018 15:42
An: NAMD list <namd-l_at_ks.uiuc.edu>; michalislaz_at_zedat.fu-berlin.de
Betreff: Re: namd-l: Weird PBC wrapping

 

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

https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

 

On Thu, Aug 30, 2018 at 6:42 AM Michail Lazaratos <michalislaz_at_zedat.fu-berlin.de <mailto:michalislaz_at_zedat.fu-berlin.de> > 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.

https://drive.google.com/file/d/1zUt5uqkdDY1LJWaPEFvcFtE9Wj0tMPXL/view?usp=sharing

https://drive.google.com/file/d/1UYpL1WBY_7xkcvFf3u7qh52EA9CzDhmY/view?usp=sharing

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,
Michael

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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