Re: AW: compress PSF into INTER

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Jun 07 2012 - 05:26:58 CDT

I have generated compressed psfs before and can assure you that there should be more in the log file than what Eduardo listed. I also trust that he would have checked his directory for additional files after exit.

On Jun 7, 2012, at 5:15 AM, Norman Geist wrote:

>> -----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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