namdenergy and bigdcd

From: Grant Schauer (
Date: Thu Jun 02 2016 - 23:58:23 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 now because namdenergy assumes we
start at the first frame and I can't pass $frame to it. Is there a
workaround for this?

Or, maybe a better question I should have started with: will namdenergy run
out of memory with very large dcds? Thank you!

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


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