evaluating energy in a trajectory of variable box size?

From: Jose Borreguero (borreguero_at_gmail.com)
Date: Tue Apr 27 2010 - 14:04:11 CDT

Dear NAMD users,

I have a trajectory (dcd format) resulting of merging 10 diffferent
trajectories, each with each own box size. Each snapshot contains its own
box size, though.
Now I want to evaluate the energy of each snapshot. I used PME and I am
passing an extended file system (box.xsc) defining a box size corresponding
to the first of the ten trajectories.
My question is whether namd will read the box size of the extended system
file and assume it is the same for every single snapshot, or if it will read
the box size of each snapshot.
The last behavior is the one I need so that namd correctly applies the
periodic boundary conditions and the PME calculations.

Here's my configuration file:

amber on
parmfile ./top
numsteps 1
switching off
scnb 2
exclude scaled1-4
1-4scaling 0.833333
outputname junk
temperature 0
COMmotion yes
cutoff 10
dielectric 1.0
extendedSystem ./box.xsc
PME on
PMEGridSizeX 60
PMEGridSizeY 54
PMEGridSizeZ 60

switchdist 10
pairInteraction on
pairInteractionGroup1 1
pairInteractionFile ./all.pdb
pairInteractionSelf on
coordinates ./all.pdb
set ts 0
coorfile open dcd dcd
while { ![coorfile read] } {
   firstTimestep $ts
   run 0
   incr ts 1
}
coorfile close

Best regards,
-Jose Borreguero

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