Re: Trouble with params file when trying to perform basic dynamics with alanine.

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Aug 30 2008 - 11:31:18 CDT

On Fri, 29 Aug 2008, Diego Alejandro Vargas wrote:

DAV> Hi everybody,
DAV> I have been attempting to run NAMD on a Linux amd64 cluster. After
DAV> installing it, I have been trying to run it. I created a configuration file
DAV> after that in pg. 114 of the manual (attached at the bottom). Below is the
DAV> command used with the resulting error. I don't understand why the parameter
DAV> file cannot be opened if it is a file that comes with the program.

diego,

that the file is bundled with the package doesn't mean anything.
more importantly, is the file alanin.params in the directory
where you are _running_ NAMD?

cheers,
   axel.

DAV>
DAV> Thank you for your attention. Feel free to ask any questions.
DAV> Diego A. Vargas
DAV>
DAV> charmrun namd2 +p2 template_alanin.conf
DAV>
DAV> Command = zcat alanin.params.Z
DAV> Filename.Z = alanin.params.Z
DAV> Command = gzip -d -c alanin.params.gz
DAV> Filename.gz = alanin.params.gz
DAV> FATAL ERROR: UNABLE TO OPEN XPLOR PARAMETER FILE alanin.params
DAV>
DAV> ------------- Processor 0 Exiting: Called CmiAbort ------------
DAV> Reason: FATAL ERROR: UNABLE TO OPEN XPLOR PARAMETER FILE alanin.params
DAV>
DAV>
DAV> ------------- Processor 0 Exiting: Caught Signal ------------
DAV> Signal: segmentation violation
DAV> Suggestion: Try running with '++debug', or linking with '-memory paranoid'.
DAV> Charmrun: error on request socket--
DAV> Socket closed before recv.
DAV>
DAV> Configuration file (template_alanin.conf):
DAV>
DAV> # protocol params
DAV> numsteps 1000
DAV>
DAV> # initial config
DAV> coordinates alanin.pdb
DAV> temperature 300K
DAV> seed 12345
DAV>
DAV> # output params
DAV> outputname /tmp/alanin
DAV> binaryoutput no
DAV>
DAV> # integrator params
DAV> timestep 1.0
DAV>
DAV> # force field params
DAV> structure alanin.psf
DAV> parameters alanin.params
DAV> exclude scaled1-4
DAV> 1-4scaling 1.0
DAV> switching on
DAV> switchdist 8.0
DAV> cutoff 12.0
DAV> pairlistdist 13.5
DAV> stepspercycle 20
DAV>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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