Weird PBC wrapping

From: Michail Lazaratos (michalislaz_at_zedat.fu-berlin.de)
Date: Thu Aug 30 2018 - 05:41:11 CDT

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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

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