visualize energy on a structure

From: Michael Zimmermann (
Date: Fri May 29 2009 - 12:20:24 CDT

Dear NAMD community,

I have been running energy minimization on a number of structures and would
like to visualize the energy on those structures as they are minimized. Say
you are viewing the molecule as ball and sticks. Then I would want the
sticks colored by their bond or torsion energy. Is there a plug-in for VMD
already made that does this? If not, is the output of NAMD energy the best
way to get that information?

Also, I was trying to use NAMD energy on a minimization I have done and
recieved the error listed below. If anyone is willing to point me in the
right direction on fixing that issue I would appreciate it.

Thank you,

Michael Zimmermann
Iowa State University

==== ERROR FROM NAMDenergy ====
abnormal program termination
    while executing
"exec $namdcmd ${jobname}-temp.namd > ${jobname}-temp.log"
    (procedure "namdrun" line 43)
    invoked from within
    (procedure "namdmain" line 76)
    invoked from within
    (in namespace inscope "::namdEnergy" script line 19)
    invoked from within
"::namespace inscope ::namdEnergy {
      mol top $currentMol
      variable sel1
      variable sel2
      variable nsel
      set energy ""
    invoked from within
".namdenergy.gobutton invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 24)
    invoked from within
"tk::ButtonUp .namdenergy.gobutton
    (command bound to event)

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