Re: [AMBER] hbond lifetime filesize issues

From: Daniel Roe <>
Date: Wed, 15 May 2019 09:36:27 -0400


On Wed, May 15, 2019 at 5:53 AM Reber, David <> wrote:
> I do get the hbwater-lifetime.dat file but it is enormous (after 10GB I stopped).
> Did I do something wrong or is this normal for a system containing many WAT? If yes, what's the best way to handle such large files in order to extract relevant information? Basically I want to compare two electrolytes and see if there's differences in hbond dynamics.

It's not impossible, especially considering you're looking at WAT-WAT
hydrogen bonds. There will be one line in the lifetime entry for each
hydrogen bond, and even with only 1000 waters that's like close to 2
million possible donor-acceptor pairs. However, what is unusual is
that you're able to write out hbavg.dat but not hbwater-lifetime.dat -
they should have the same number of lines. Are you sure the file
that's gigantic isn't hbseries.gnu? I could easily see the time series
file getting out of control.


> Thank you in advance for any hints!
> David
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Received on Wed May 15 2019 - 07:00:02 PDT
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