Re: Incorrect periodic box imaging with AMBER parameters

From: nordgren_at_sas.upenn.edu
Date: Thu Aug 04 2005 - 17:40:58 CDT

Hi Grzegorz,

It certainly seems like something simple is messed up with your coord
wrapping.

Just to be clear... you have tried setting the "CellOrigin" parameter to
the actual coords of the geometric center of your system, instead of (0 0 0),
and you still see strange coords output?

If you turn off the "WrapAll" and "WrapNearest" flags, does that fix things?

- Erik

C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania

Quoting surendra negi <negi009_at_yahoo.com>:

> 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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