Replica Exchange NAMD

From: Dirar Homouz (dirar_at_hotmail.com)
Date: Tue Nov 13 2007 - 12:09:52 CST

I'm running the replica exchange method on namd using the tcl script "replica_exchange.tcl" on a linux cluster:
 
"Linux farnsworth1.phys.uh.edu 2.6.9-42.0.2.ELsmp #1 SMP Wed Aug 23 13:38:27 BST 2006 x86_64 x86_64 x86_64 GNU/Linux".
 
The command in the batch file looks like this:
 
tclsh ../replica_exchange.tcl /home/dirar/replica/example/fold_alanin.conf
 
The run doesn't go through, I get the following error message:
 
FATAL ERROR: Simulation config file is not accessible.
 
The log file looks like this:
 
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 50900 for mpi-linux-amd64
Info: Built Thu Jun 28 09:51:39 CDT 2007 by root on farnsworth1.phys.uh.edu
Info: 1 NAMD 2.6 Linux-amd64-MPI 1 compute-0-8.local dirar
Info: Running on 1 processors.
Info: 7896 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Found 2 config files.
Info: Configuration file is +netpoll
FATAL ERROR: Simulation config file is not accessible.
Stack Traceback:
  [0] CmiAbort+0x2b [0x75f899]
  [1] _Z8NAMD_diePKc+0x4a [0x4a630a]
  [2] main+0x1f5 [0x4a9445]
  [3] __libc_start_main+0xdb [0x345dd1c3fb]
  [4] fmod+0xaa [0x4a5c0a]
 
 
 
Dirar
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