VMD-L Mailing List

From: Mintare Cesiunaite (mcesiun_at_iu.edu)
Date: Tue Jun 16 2020 - 23:15:36 CDT

Dear VMD writers,

I am using VMD extension Force Field Toolkit to train on Ethanol. Presently
I am stuck at the step of Bond&Angle optimization. This particular step
required NAMD2 installed to run in the background for the calculations.
This is what I did:
1) I downloaded zip file of NAMD_2.13 and extracted it into directory on
Desktop (since it is said Namd2 can be unzipped and can be run directly)
2) I opened Tk Console and led it to the NAMD_2.13 directory on the desktop
(.....cd Desktop -> cd NAMD_2.13)
3) I uploaded the input files (psf, pdb, hess.log, par) in the input
section and I selected namd2.exe that is in the NAMD_2.13 directory on my
Desktop

When I run optimization, I get "Child killed: unknown signal" error.
I have tried placing namd2.exe in different locations as Program files, but
still get the same error.

I suspect there is miscommunication between the VMD and NAMD2.

This is the Details of the error:

child killed: unknown signal
child killed: unknown signal
    while executing
"::exec {C:/Program Files/NAMD_2.13_Win64-multicore/namd2.exe}
min-bondangles.conf"
    ("eval" body line 1)
    invoked from within
"eval ::exec [list $exec_path] [lrange $args 1 end]"
    (procedure "::ExecTool::exec" line 14)
    invoked from within
"::ExecTool::exec $namdbin $minName.conf"
    (procedure "::ForceFieldToolKit::BondAngleOpt::optBondsAngles" line 68)
    invoked from within
"$function $p0list"
    (procedure "construct_initial_simplex" line 22)
    invoked from within
"construct_initial_simplex [lindex $args 0] $scale"
    (procedure "::Optimize::Opt0::handle" line 91)
    invoked from within
"$opt initsimplex $baInitial $scale"
    (procedure "::ForceFieldToolKit::BondAngleOpt::optimize" line 324)
    invoked from within
"::ForceFieldToolKit::BondAngleOpt::optimize"
    (procedure "::ForceFieldToolKit::gui::baoptRunOpt" line 40)
    invoked from within
"::ForceFieldToolKit::gui::baoptRunOpt "
    invoked from within
".fftk_gui.hlf.nb.bondangleopt.runOpt invoke "
    invoked from within
".fftk_gui.hlf.nb.bondangleopt.runOpt instate {pressed !disabled} {
.fftk_gui.hlf.nb.bondangleopt.runOpt state !pressed;
.fftk_gui.hlf.nb.bondangleopt...."
    (command bound to event)

I am not sure how to solve it or how to "install NAMD2 correctly. I use
Windows 10.

Thank you for your assistance.

Sincerely,
Mintare Cesiunaite
Student in IUPUI