AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on"

From: Grzegorz Jezierski <>
Date: Tue, 31 May 2005 18:04:20 +0200

Dear Amber 8 users,
I created my system using LeaP provided with AMBER 8 distribution, and
the old format of parameter file.
During a short MD I ran using Amber 8 (and Amber 6), water molecules did
not stay inside the box. This is something I didn't encounter using
Amber 6's LeaP.
Periodic Boundary Conditions were applied to a small hydrated DNA
fragment neutralized with Na ions. When constant pressure was used, most
of H20 "crept out" of the box like there were no PBC cell images. In
contrast, when I used constant volume, single H2O molecules appeared far
outside the box.
When I ran 1 ns MD of a similar, but somewhat bigger system
(volume=const.), water spread out over a large space, but empty spaces,
corresponding to translational images of the solute, were left!
I would say that no box information was passed in .TOP (parameter) file,
but its last line says:

  9.00000000E+01 3.95462090E+01 4.59628260E+01 3.57232720E+01

Thank you for help
Grzegorz Jezierski

Below: input file for p=const (2nd stage of MD), and input for LEAP.

# MD Ewald test
  ntb=2, imin=0, nmropt=0,
  ntx=5, irest=1,
  ntwx=1000, ntwv=1000, ntave=1000, ntwr=1000,
  cut=8.0, scnb=2.0, scee=1.2,
  ntt=1, tautp=0.4, TEMP0=298.0,
  dt=0.002, nstlim=10000,
  ntc=2, ntf=2,
  nfft1=40, nfft2=40, nfft3=40,
  order=4, ew_type=0,
verbosity 2
source leaprc.ff98
set default OldPrmtopFormat on

test = loadpdb test.pdb
addions test Na+ 0
solvatebox test TIP3PBOX 8.0
saveAmberParm test test.crd
savePdb test test_NEW.pdb


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Received on Tue May 31 2005 - 17:53:00 PDT
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