Tutorial-l Mailing List

From: Alia Sagatova (sagal239_at_student.otago.ac.nz)
Date: Mon May 13 2013 - 20:33:55 CDT

 Hi,

I've started going through the tutorial for NAMD and when I got to the step where I have to run the simulation for minimization and equilibration of the UBQ molecule, I got this error message:

1-2-sphere alia$ namd2 ubq ws eq.conf > ubq ws eq.log &
Charm++: standalone mode (not using charmrun)
Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21
Charm++> scheduler running in netpoll mode.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (4-way SMP).
Charm++> cpu topology info is gathered in 0.000 seconds.
Info: NAMD 2.9 for MacOSX-x86_64-multicore
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
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 60400 for multicore-darwin-x86_64
Info: Built Mon Apr 30 14:00:10 CDT 2012 by jim on bogota.ks.uiuc.edu
Info: 1 NAMD 2.9 MacOSX-x86_64-multicore 1 ou093198.otago.ac.nz alia
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.02334 s
FATAL ERROR: No simulation config file specified on command line.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: No simulation config file specified on command line.

[0] Stack Traceback:
  [0:0] 0 namd2 0x000000010062dec8 CmiAbort + 134
  [0:1] 1 namd2 0x00000001000327c0 _Z8NAMD_diePKc + 80
  [0:2] 2 namd2 0x00000001000354ce _Z18after_backend_initiPPc + 1326
  [0:3] 3 namd2 0x00000001000355a6 main + 38
  [0:4] 4 namd2 0x0000000100001494 start + 52
  [0:5] 5 ??? 0x0000000000000001 0x0 + 1
Charm++ fatal error:
FATAL ERROR: No simulation config file specified on command line.

[0] Stack Traceback:
  [0:0] 0 namd2 0x000000010062cf70 charmrun_abort + 63
  [0:1] 1 namd2 0x000000010062deff CmiAbort + 189
  [0:2] 2 namd2 0x00000001000327c0 _Z8NAMD_diePKc + 80
  [0:3] 3 namd2 0x00000001000354ce _Z18after_backend_initiPPc + 1326
  [0:4] 4 namd2 0x00000001000355a6 main + 38
  [0:5] 5 namd2 0x0000000100001494 start + 52
  [0:6] 6 ??? 0x0000000000000001 0x0 + 1
Abort trap: 6
logout

[Process completed]

I'm running this on a MAC OS X version 10.7.5. I also tried running it in Windows 7 but I got the same problem. I'm not really sure how to fix this. Do I have t download CHARM separately for this? Your help would be much appreciated.

Kind Regards,
Alia Sagatova

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