From: Cruz-Chu Eduardo Roberto (eduardo.cruz_at_mavt.ethz.ch)
Date: Thu Jun 07 2012 - 04:20:56 CDT
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.
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
> 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.
> that is "b) add a field "genCompressedPsf on" in the configuration
> 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
We need some detail to identify the problem.
> Does anyone has an example?, a namd configuration file I can use as
> Below, I am attaching my namd configuration, the one that did not work.
> Any help, it would be really appreciated.
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