From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jun 07 2012 - 05:15:09 CDT
> -----Ursprüngliche Nachricht-----
> Von: Norman Geist [mailto:norman.geist_at_uni-greifswald.de]
> Gesendet: Donnerstag, 7. Juni 2012 12:12
> An: 'Cruz-Chu Eduardo Roberto'
> Cc: Namd Mailing List (namd-l_at_ks.uiuc.edu)
> Betreff: AW: namd-l: compress PSF into INTER
>
> Hi,
>
> I'm sorry to tell you that you haven't followed the tutorial very
> carefully. The keyword "genCompressedPsf on" does only generate a new
> compressed psf when running namd and than exits. To use the new
> compressed psf afterwards, you need to specify "useCompressedPsf on"
> and remove the "genCompressedPsf on" from the conf. Also use
> structure.inter instead of structure in the conf. Also you should use
> bincoordinates instead of coordinates which means that you have to
> convert your non binary pdb or coor to a binary one (using vmd).
>
> So the bottom line is it's two steps:
>
> 1. Generate a compressed psf with namd and genCompressedPsf on" and a
> binary coordinate file with vmd.
> 2. Run memopt namd with "useCompressedPsf on"
and structure.inter
I forgot to mention.
>
> I hope I got it right.
>
> Good luck.
>
> For more information look at
> http://www.ks.uiuc.edu/Research/namd/wiki/?NamdMemoryReduction
>
> Norman Geist.
>
>
> > -----Ursprüngliche Nachricht-----
> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> > Auftrag von Cruz-Chu Eduardo Roberto
> > Gesendet: Donnerstag, 7. Juni 2012 11:21
> > An: Norman Geist
> > Cc: Namd Mailing List
> > Betreff: RE: namd-l: compress PSF into INTER
> >
> > Hi Norman;
> >
> > NAMD just halts after reading the PSF file, then NAMD crashes. The
> > last line of the log file are:
> >
> > Info: 0 VDW_PAIRS
> > Info: 0 NBTHOLE_PAIRS
> > Info: TIME FOR READING PSF FILE: 34.5907
> >
> > My desktop has 16 GB of memory, so it should handle the PSF/COOR
> files,
> > which are less than 2GB of data.
> >
> > Below I am attaching the log file.
> >
> > Have you (or anyone) successfully used the "genCompressedPsf on"
> option
> > to generate an INTER file?. I pay a beer for any positive answer.
> >
> > Regards;
> >
> > Eduardo
> > ________________________________________
> > From: Norman Geist [norman.geist_at_uni-greifswald.de]
> > Sent: Thursday, June 07, 2012 8:24 AM
> > To: Cruz-Chu Eduardo Roberto
> > Cc: Namd Mailing List
> > Subject: AW: namd-l: compress PSF into INTER
> >
> > > -----Ursprüngliche Nachricht-----
> > > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> > > Auftrag von Cruz-Chu Eduardo Roberto
> > > Gesendet: Mittwoch, 6. Juni 2012 20:38
> > > An: namd-l_at_ks.uiuc.edu
> > > Betreff: namd-l: compress PSF into INTER
> > >
> > > Hi;
> > >
> >
> > Hi
> >
> > >
> > > I am trying to run a 6 million atom system. For that, I need to
> >
> > Wow, that's heavy. My biggest system has 1.5 million ^^
> >
> > > compress the PSF file into a INTER file. The NAMD wiki provide
> some
> > > brief explanation.
> > >
> > >
> > >
> >
> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdMemoryReductio
> > > n
> > >
> > >
> > > that is "b) add a field "genCompressedPsf on" in the configuration
> > > file".
> > >
> > >
> > > well, I did it using NAMD 2.8 and also NAMD 2.9. I also compiled
> NAMD
> > > with --with-memopt flag, and no success.
> >
> > What exactly does "no success" mean? Is namd crashing with an error
> or
> > something?
> > We need some detail to identify the problem.
> >
> > Regards
> >
> > Norman
> >
> > >
> > >
> > > Does anyone has an example?, a namd configuration file I can use as
> > > guide?.
> > >
> > >
> > > Below, I am attaching my namd configuration, the one that did not
> > work.
> > >
> > >
> > > Any help, it would be really appreciated.
> > >
> > >
> > > Regards;
> > >
> > >
> > > Eduardo
> > >
> > >
> >
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