Thank you very much, I will give that a try.
Best regards
David
> -----Original Message-----
> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> Sent: Dienstag, 21. Mai 2019 18:51
> To: AMBER Mailing List
> Subject: Re: [AMBER] hbond lifetime filesize issues
>
> Hi,
>
> Sorry for the delay in replying.
>
> On Thu, May 16, 2019 at 1:02 AM Reber, David <David.Reber.empa.ch>
> wrote:
> >
> > 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?
>
> Why not just skip writing the hbseries.gnu file at all? Just do the
> analysis on the sets in-memory. If you don't have enough memory, maybe
> try switching to the plain .dat format or try caching the series data
> sets in memory (requires a recent version of cpptraj with the
> 'usediskcache' command - use it right before the 'hbond' command).
>
> Also, if what you're looking for are the average behavior of water
> around the ions, I recommend using the 'solventdonor' and
> 'solventacceptor' keywords for water. In other words, since you don't
> care which particular water is around sodium, you don't need to track
> each individual one. This will greatly cut down on the number of data
> sets generated, and is probably more what you actually want. So
> something like:
>
> hbond sodium :Na+ solventdonor :WAT solventacceptor :WAT.O out
> hbna.dat avgout hbnaavg.dat dist 4 angle -1 nointramol series
> lifetime sodium name nalife out nalife.dat
>
> Hope this helps,
>
> -Dan
>
>
> >
> > 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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Received on Tue May 21 2019 - 19:30:02 PDT
