Hello again
Ok, so I can't finish writing the hbseries.gnu file before I run out of memory. In order to assess lifetimes, is it completely wrong to take hbavg.dat and then take the average of the frames column? In my case 1 frame per ps --> average hbond lifetime in ps?
I'm also trying to look at residence times of WAT around ions. I use
trajin MD333.mdcrd
hbond sodium donormask :Na+ acceptormask :WAT.O out hbna.dat avgout hbnaavg.dat dist 4 angle -1 nointramol
go
in hbnaavg.dat I get this:
#Acceptor DonorH Donor Frames Frac AvgDist AvgAng
Na+_688.Na+ WAT_955.H1 WAT_955.O 16873 0.3375 2.6007 51.0838
Na+_688.Na+ WAT_955.H2 WAT_955.O 16873 0.3375 2.6007 52.0804
Na+_600.Na+ WAT_1043.H2 WAT_1043.O 14103 0.2821 2.6007 50.9209
Na+_600.Na+ WAT_1043.H1 WAT_1043.O 14103 0.2821 2.6007 51.1632
...
Where I can delete every other line. Again, is it completely wrong to take the average of the frames column in order to compare the average residence time of WAT around Na+ in different systems?
Thank you very much in advance,
David
> -----Original Message-----
> From: Reber, David [mailto:David.Reber.empa.ch]
> Sent: Donnerstag, 16. Mai 2019 03:52
> To: AMBER Mailing List
> Subject: Re: [AMBER] hbond lifetime filesize issues
>
> 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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> >
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Received on Wed May 15 2019 - 22:30:02 PDT
