Take a look at the tutorial
http://amber.scripps.edu/tutorials/basic/tutorial1/index.htm
If you look at the individual snapshot structures,
the substituents of the bases are not always
in the plane of the base and fluctuate.
However, if you calculate average structures (see tutorial B3
how to do this), this should become better.
best regards,
mathy
---------------
On Wed, 4 Jul 2007, Sophie Barbe wrote:
>
>
> Dear amber users,
>
> I am performing molecular dynamics simulations of DNA double-strands( with
> AMBER9). I use the amber force field refined for nucleic acids : parmbsc0.
> My procedure is the following one :
> - preparation of MD : initial minimization followed by slow heating to 310K at
> constant volume over a period of 100 ps using harmonic restraints (25 kcal...)
> on the solute atoms. These restraints are slowly relaxed from 10 to 1 kcal.. :
> - first during an equilibration at constant volume
> - secondly during 8 segments of equilibration using constant temperature (310 K)
> and pressure (1 bar) conditions via the Berendsen algorithm with a coupling
> constant of 0.2 ps for both parameters.
> The final segment consists of 50ps unrestrained equilibration.
> The simulations are then continuing at constant temperature and pressure
> conditions, using Beredsen algorithm with a coupling constant of 2 ps for both
> parameters.
> I notice that the nucleic bases are not planar. The substituents of the bases
> are out of plane (dihedral angle > 10 deg).
>
> Thank you for advance for your answers
>
> Sophie
>
>
>
>
>
>
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Received on Sun Jul 08 2007 - 06:07:10 PDT
