VMD-L Mailing List
From: Grant Schauer (grantschauer_at_gmail.com)
Date: Fri Jun 03 2016 - 15:55:26 CDT
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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
Grant
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
bigdcd_wait
quit
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