RE: A bug in replica.namd?

From: Ada Zhan (
Date: Thu Nov 08 2012 - 13:32:39 CST

Hi folks,

I modified the replica.namd to walk around the problem mentioned in my previous email. Since that part is only related to the creation of a .tcl file that has nothing to do with the running exchange simulation, I changed the file name of the file to be written in the script so that it won't interfere with other parts of the script. The following is what I revised and I also attach my modified version,

 ("while" body line 69)
    invoked from within
"while {$i_run < $num_runs} {
       set rfile [open [format "$restart_root.$replica_id.$replica_id.tcl" $replica_id] "w"]
       set oldroot [format $old_restart_root $replica_id]
       file delete $oldroot.$replica_id.$replica_id.tcl

If you guys have better suggestions, please bring them up! Thanks!
Good luck, everyone!


Subject: namd-l: A bug in replica.namd?
Date: Wed, 7 Nov 2012 15:37:13 -0700

I am testing the replica exchange with abf in namd 2.9.
It works for many steps initially until the following message:
TCL: expected integer but got ""
FATAL ERROR: expected integer but got ""
    while executing
"format "$restart_root.tcl" """
    ("while" body line 69)
    invoked from within
"while {$i_run < $num_runs} {

  run $steps_per_run
  incr i_step $steps_per_run
  set TEMP $saved_array(TEMP)
  set POTENTIAL [expr $save..."
    (file "~/NAMD_2.9_Source/lib/replica/replica.namd" line 98)
    invoked from within
"source ~/NAMD_2.9_Source/lib/replica/replica.namd "
    invoked from within
"if { ! [catch numPes] } { source ~/NAMD_2.9_Source/lib/replica/replica.namd }"

I checked the replica.namd script. The error happens at the line :

set rfile [open [format "$restart_root.tcl" ""] "w"]

There is indeed a "" after "format ...". But what integer should be expected here ? Is that a bug in this script?

Thanks, all!

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:44 CST