RE: compress PSF into INTER

From: Cruz-Chu Eduardo Roberto (eduardo.cruz_at_mavt.ethz.ch)
Date: Thu Jun 07 2012 - 04:20:56 CDT

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?NamdMemoryReduction > > > 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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