Re: NAMD: run problem

From: Peter Freddolino (
Date: Wed Jun 21 2006 - 18:22:17 CDT

Hi Bo,
just to check, was there no output to the console you ran it from after
it crashed? The way you have it set up, some errors will be printed to
the terminal, not the log file. Also, could you please run top at a
console and confirm that there are no namd2 processes sitting around?

bo baker wrote:
> Hello, NAMD:
> I try to do some test run with NAMD. I use same .conf file for the two
> runs. The first one went through without any problem. But when I use
> the same .conf file (with change on the output file name), this time,
> the run stops at 223 step, and does not go futher anymore. I don't
> understand what is going on, and where is the problem, and how can I
> fix.
> Here is how I did:
> ~ bakerby$ cd /Applications/NAMD_2.6b1_MacOSX-PPC
> ~ bakerby$ export DYLD_LIBRARY_PATH='/Applications/NAMD_2.6b1_MacOSX-PPC'
> ~ bakerby$ /Applications/NAMD_2.6b1_MacOSX-PPC/namd2 test.conf >
> test3.log &
> [1] 292
> I have the conf and log files attached.
> Thank you for your help.
> Bo

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