From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri May 15 2009 - 09:44:57 CDT

Hi Anna,
it looks like your namd binary wasn't built with tcl support. While you
can get namd to work this way, many features will be disabled, and the
syntax in the tutorials assumes a fully functional build. I'd recommend
either rebuilding with tcl support or using one of the precompiled
binaries available on the namd website.
Best,
Peter

Anna Dejardin wrote:
> Hi Peter,
>
> Here is the logfile:
>
> Charm++> Running on MPI version: 1.2 multi-thread support: 1/0
> Charm warning> Randomization of stack pointer is turned on in Kernel,
> run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable
> it. Thread migration may not work!
> Info: NAMD 2.6 for Linux-amd64-MPI
> Info:
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
> Info:
> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 60000 for mpi-linux-amd64-pgf90-mpicxx
> Info: Built Tue May 5 12:36:23 BST 2009 by atg on reinette.lcn.ucl.ac.uk
> Info: 1 NAMD 2.6 Linux-amd64-MPI 1 reinette.lcn.ucl.ac.uk acd
> Info: Running on 1 processors.
> Info: 1592 kB of memory in use.
> Info: Memory usage based on mallinfo
> Info: Changed directory to
> /homes/acd/NAMD2.6/namd-tutorial-files/1-2-sphere
> Info: Configuration file is ubq_ws_eq.conf
> ERROR: Expecting value and optional units for option 'temperature'
> ERROR: Expecting value and optional units for option 'langevinTemp'
> ERROR: The following variables were set in the
> ERROR: configuration file but are NOT VALID
> ERROR: run
> ERROR: reinitvels
> ERROR: minimize
> ERROR: set
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
> p0_14453: p4_error: : 1
>
> Thanks
>
> Anna
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