Problems with tcl scripts for REMD simulation

From: Wei Huang (
Date: Fri Apr 16 2010 - 15:41:25 CDT

Dear NAMD experts,

I am trying to set up REMD simulation with the tcl scripts come with NAMD2.7b2. I am able to run REMD simulation using the input files in the example directory with 8 CPU cores in the PBS queue. However, when I run 16 replicas (1 replica/core), the PBS job seems to be running but no outputs are generated except the log files and nrc files. After the PBS job finishes, I get the following error message in every log files:

FATAL ERROR: disconnect server
    while executing
"error "disconnect server""
    ("while" body line 9)
    invoked from within
"while { 1 } {
        while [catch {gets $server_channel cmd} rval] {
puts $errorCode
          if {![string match "POSIX EINTR*" $errorCode]} {
    (file "fold_alanin.job0.0.log.nrc" line 11)
[0] Stack Traceback:
  [0] CmiAbort+0x5f [0xabcdf3]
  [1] _Z8NAMD_diePKc+0x62 [0x509172]
  [2] _ZN9ScriptTcl3runEPc+0x54 [0x97142a]
  [3] _Z18after_backend_initiPPc+0x22b [0x50d98b]
  [4] main+0x3a [0x50d72a]
  [5] __libc_start_main+0xdb [0x345b61c3fb]
  [6] _ZNSt8ios_base4InitD1Ev+0x52 [0x508ada]

Could some one help me figure out what the problem could be? Thanks! Please let me know if I didn't provide enough information for troubleshooting.


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