VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Mar 30 2015 - 13:30:36 CDT

Please CC VMD-L on correspondences so that everyone can benefit from the discussion.

You have to change the offending entry in the parameter file that you are passing into NAMDEnergy.

Regards,
Christopher Mayne

On Mar 30, 2015, at 11:34 AM, Subrata Paul wrote:

Thanks Christopher,

How can i change the periodicity in VMD NAMDenergy pluging

On Mon, Mar 30, 2015 at 7:56 PM, Mayne, Christopher G <cmayne2_at_illinois.edu<mailto:cmayne2_at_illinois.edu>> wrote:
It appears that there is something amiss with the parameter file(s) you're passing into NAMDEnergy via the -par option. The error message suggests that one of the dihedral parameters contains a periodicity of zero (n=0). Normal values are 1, 2, 3, 4, and/or 6.

Regards,
Christopher Mayne

On Mar 30, 2015, at 12:26 AM, Subrata Paul wrote:

Dear NAMD/VMD user,

I am calculating nonbonded energy from amber topology file usind VMD NAMDenergy plugin.
The following error are coming

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: The periodicity of dihedral # 1 is zero!

Charm++ fatal error:
FATAL ERROR: The periodicity of dihedral # 1 is zero!

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: The periodicity of dihedral # 1 is zero!

Charm++ fatal error:
FATAL ERROR: The periodicity of dihedral # 1 is zero!

    while executing
"exec $namdcmd ${jobname}-temp.namd > ${jobname}-temp.${i}.log"
    (procedure "namdrun" line 75)
    invoked from within
"namdrun"
    (procedure "namdmain" line 76)
    invoked from within
"namdmain"
    (in namespace inscope "::namdEnergy" script line 19)
    invoked from within
"::namespace inscope ::namdEnergy {
      mol top $currentMol
      variable sel1
      variable sel2
      variable nsel
      set energy ""
      set..."
    invoked from within
".namdenergy.gobutton invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 22)
    invoked from within
"tk::ButtonUp .namdenergy.gobutton"
    (command bound to event)

Can you suggest me why..? 

--
With Best Regards
Subrata Paul
PhD Student
Dept of Chemistry.
IIT Guwahati
--
With Best Regards
Subrata Paul
PhD Student
Dept of Chemistry.
IIT Guwahati