execute vs. config directory

From: Thomas C. Bishop (bishop_at_latech.edu)
Date: Fri Sep 14 2012 - 15:07:24 CDT

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

thanks
TOm

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