Re: Weird PBC wrapping

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Aug 30 2018 - 08:41:54 CDT

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> 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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