From: Grant Schauer (
Date: Fri Jun 03 2016 - 15:55:26 CDT

Hi all,

I tried to run namdenergy on a very large trajectory with bigdcd (see
below), but it seems to be just looping over the same first two frames on
repeat, which maybe makes some sense because namdenergy assumes I start at
the first frame and I can't pass $frame to it.

Is there a workaround for this? Alternatively, is there a way for
namdenergy to handle large dcds frame-by-frame?

Any help appreciated, thanks

source bigdcd.tcl
package require namdenergy

set mol [mol new ./molecule.psf type psf waitfor all]

mol addfile ./molecule.pdb type pdb waitfor all
set sel1 [atomselect top protein]
set sel2 [atomselect top nucleic]

proc energies {frame} {
global mol sel1 sel2 out

namdenergy -nonb -vdw -elec -sel $sel1 $sel2 -ofile out.dat -par
par_all27_prot_na.prm -par

bigdcd energies dcd ./giant_dcd.dcd