From: Charles Danko (dankoc_at_gmail.com)
Date: Mon Jul 25 2005 - 08:32:20 CDT
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> 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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