Hi Dan
Thanks for your reply. You are right, it's the hbseries.gnu file that gets that big. I assume I can try to let it finish and once hbwater-lifetime.dat is written I can delete hbseries.gnu? Or can you recommend anything else to tackle large files?
Thanks and best regards
David
> -----Original Message-----
> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> Sent: Mittwoch, 15. Mai 2019 15:36
> To: AMBER Mailing List
> Subject: Re: [AMBER] hbond lifetime filesize issues
>
> Hi,
>
> On Wed, May 15, 2019 at 5:53 AM Reber, David <David.Reber.empa.ch>
> 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.
>
> -Dan
>
> >
> > Thank you in advance for any hints!
> > David
> >
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Received on Wed May 15 2019 - 19:00:02 PDT
