From: Ada Zhan (zyqfrog10_at_msn.com)
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.$replica_id.tcl
.....
}"
If you guys have better suggestions, please bring them up! Thanks!
Good luck, everyone!
-Ada
From: zyqfrog10_at_msn.com
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: A bug in replica.namd?
Date: Wed, 7 Nov 2012 15:37:13 -0700
I am testing the replica exchange with abf in namd 2.9.
It works for many steps initially until the following message:
====
TCL: expected integer but got ""
FATAL ERROR: expected integer but got ""
while executing
"format "$restart_root.tcl" """
("while" body line 69)
invoked from within
"while {$i_run < $num_runs} {
run $steps_per_run
save_array
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!
-Ada
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