AW: execute vs. config directory

From: Norman Geist (
Date: Mon Sep 17 2012 - 01:47:22 CDT


Von: [] Im Auftrag
von Aron Broom
Gesendet: Freitag, 14. September 2012 22:51
An: Thomas C. Bishop
Betreff: Re: namd-l: execute vs. config directory


well, as long as you are correctly specifying the path, it should run with
the config file. That being said, any file location definitions within the
config file are relative to the path where the config file is found NOT the
path of the NAMD executable.

IMHO not. I would say that the path of the config file doesn't affect
anything. I guess the CWD (current work directory) of the namd2 executable
is the point where the relative paths in the config file are resolved from.

Norman Geist.


On Fri, Sep 14, 2012 at 4:07 PM, Thomas C. Bishop <
<>> wrote:

Can someone please tell how the command line call to namd
may or may not affect it's notion of the working & execution directories.
I seem to run into a gotcha every once in awhile so I'm missing something.

to be specific how might these command lines affect namd runs
if dyn1.conf contains relative path names for inputs and outputs

namd2 dyn1.con
namd2 /somepath/dyn1.conf
namd2 ../otherdirectory/dyn1.conf
./bin/namd2 w/ the above command line args
charmrun w/ the above command line args


   Thomas C. Bishop
    Tel: 318-257-5209
    Fax: 318-257-3823
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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