From: surendra negi (negi009_at_yahoo.com)
Date: Thu Aug 04 2005 - 16:11:15 CDT
try following commands in VMD
measure minmax $t
# then calculate cellBasisVector1 =abs|x1+x2|/2
# and box center by
measure center $t
best, surendra
--- Grzegorz Jezierski
<jezierski_at_theochem.tu-muenchen.de> wrote:
> Hi,
> I tried centering the system as well as many other
> tricks, but to no avail.
> I know there's a new version of NAMD coming, but I
> don't think they
> fixed this.
> Any hints?
>
> Charles Danko wrote:
>
> > Hello,
> >
> > It was my understanding that cellOrigin should be
> the center of the
> > periodic box, not 0 0 0. Try changing it to the
> geometric center of
> > the box. You should be able to calculate this
> easily for your system
> > in VMD. If you have trouble, search google, or
> post again.
> >
> > Regards,
> > Charles Danko
> >
> > On 7/25/05, *Grzegorz Jezierski*
> <jezierski_at_theochem.tu-muenchen.de
> > <mailto:jezierski_at_theochem.tu-muenchen.de>> wrote:
> >
> > 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
> > displaced.
> > 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
> > parmfile T3.top
> > ambercoor T3.center.rst
> >
> > 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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