From: Grzegorz Jezierski (jezierski_at_theochem.tu-muenchen.de)
Date: Thu Aug 04 2005 - 13:04:05 CDT
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
>
> ================================================
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:39:47 CST