From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jun 07 2012 - 05:11:54 CDT
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"
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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