Incorrect periodic box imaging with AMBER parameters

From: Grzegorz Jezierski (
Date: Mon Jul 25 2005 - 04:11:20 CDT

Dear NAMD users,
While running NAMD simulations on DNA immersed in water, and using AMBER
forcefield, I encountered the following problem:
During the first step of calculation (MD or minimization), the initial
periodic box was split in 4 smaller boxes and displaced by a half of box
dimension, plus the structure was reflected in mirror planes along the
main axes. The DNA duplex was split into 2 individual chains and also
When a box is smaller than a cube with 25 A long side, no reflection
occurs, just displacement. Then, during subsequent steps of simulation,
the system behaves correctly. This problem is seen only when Periodic
Boundary Conditions are on.
Having performed numerous tests and trials I think this might be a bug
in NAMD code, but before submitting a report I want to ask if someone
has had similar problems?
Thank you
G. Jezierski

PS. Below a configuration file:
# ==== NAMD 2.5 ==== EM TEST ==== DNA IN WATER ====
bincoordinates em_test.coor
parameters /parameters/toppar/par_amber_98.inp

paraTypeCharmm off
Amber yes

outputName em_test
outputEnergies 10
wrapAll on
wrapNearest on

numsteps 10

dielectric 1.0
switching off
switchDist 9.0
cutoff 10.0
pairlistdist 12.0
margin 1.0
exclude scaled1-4
1-4scaling 0.833333
scnb 2

cellBasisVector1 50.2 0.0 0.0
cellBasisVector2 0.0 47.9 0.0
cellBasisVector3 0.0 0.0 59.2
cellOrigin 0 0 0

Pme on
PmeGridsizeX 50
PmeGridsizeY 50
PmeGridsizeZ 60

minimization on


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