Periodic Boundary Conditions and Wrap

From: Joshua D. Moore (
Date: Tue Jun 28 2005 - 03:31:38 CDT


I am currently running an NPT simulation of ethanol and water. I have ran
my simulation for approximately 2 ns now, and I have a question concerning
the DCD trajectory file, boundary conditions and Wrap.

I did not specify WrapAll or WrapWater in my configuation file, so these
should be turned off by default. I calculated the radial distribution
function between the centers of mass of all of my ethanol molecules from
the DCD file. At first I neglected to consider the wrapping (or lack of
since I didn't specify WrapAll, etc) of my molecules. However, after I
took this into account, but I do not see any change.

Also, when I observe my trajectories in VMD, I do not (or I do not think
I) observe anything crossing system boundaries. I am only considering 64
and 512 ethanol molecules, and my cubic box length is around 40 - 46

Does NAMD automatically wrap molecules when writing DCD files despite
having WrapAll or WrapWater turned off? Or is there something I am not
considering in the barostat that is affecting the wrapping or periodic
boundary conditions? I am using a Langevin temperature and pressure
control with the following parameter:

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature

Many thanks.

Joshua Moore

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