Re: launch NAMD from tcl script - bug?

From: Floris Buelens (
Date: Wed Jun 24 2009 - 10:54:24 CDT

Thanks but no good I'm afraid... turns out there's only a problem when running with charmrun, everything works as I'd expect when running standalone.
I don't know if anyone else will care about this but it looks like a bug... with these TCL commands:

run 0
[exec ~/namd2]

.. I get the expected behaviour ("No simulation config file specified") with namd standalone, but with [~/charmrun ++local +p1 ~/namd2 conffile.conf] it doesn't get that far. I've tried with v2.6 and 2.7. On an x86_64 system (with release binaries of 2.7 and my builds of 2.6 and 2.7) I get "error reading output from command: interrupted system call". On 32-bit i686-icc and MacOSX-i686-g++ it just hangs when run with charmrun.
Thanks for your time,


From: J Liu <>
To: Floris Buelens <>
Sent: Wednesday, 24 June, 2009 14:58:47
Subject: Re: namd-l: launch NAMD from tcl script

Hi Buelens:
Please have a try with "eval exec ~/namd2 alt.conf".

Jian Liu
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----- Original Message -----
From: Floris Buelens <>
Subject: namd-l: launch NAMD from tcl script
Date: 2009-6-24 19:55:06


I'm trying to script some 'live' analysis in TCL - what I want to do is save coordinates with 'output', then start another instance of NAMD to do a single-frame calculation with different parameters. I thought I could do this along the lines of "exec ~/namd2 alt.conf" but I get "error reading output from command: interrupted system call"... what am I doing wrong?
thanks a lot!



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