Animations in Biochemistry
Here is a collection of Mpeg animations regarding problems
treated in the
Biochemistry and Biophysics group ;
all these animations are based on raw data calculated at
and are generated with the molecular graphics code
Here follows a brief description of some Mpeg files;
This stick representation of a Cytosine molecule moves according to
three low-frequency vibrational normal modes; the determination of
the vibrational normal frequencies of a molecule permits to determine
the zero-point motion of the system and also its infrared vibrational
spectrum, which can be directly compared with the experimental
This movie shows the water octamer in one of its minimum energy
configurations. Several types of graphical representations are shown,
namely wire, wire with labels, stick, stick with
h-bonds (the blue ones), stick and ball.
This movie is a stick'n ball representation of
Ab-Initio Molecular Dynamics data, showing the proton
exchange between two H2O systems.
This method solves the Schroedinger equation, that is
the equation of motion of the Quantum Mechanics. This
method is therefore very precise and allows
to describes phenomena which are not observable
in a classical description of the nature.
This Mpeg movie show the minimization of a MET-enkephalin peptide,
that is the searching of the minimum energy conformation for this
molecule in a given surrounding (in this case the vacuum).
Here is a Molecular Dynamics run of a fragment of BPTI
(Bovine Pancreatic Tripsine Inibitor) surrounded by
water molecules. The Molecular Dynamics method solves
the newtonian equations of motion, giving therefore a
'classical' description of the system; this is much less
computationally demanding, with respect to quantum
methodologies, and can be applied to systems composed by several
hundreths of atoms.
This movie shows how a protein can be 'built' using
GMC code. It is possible to combine several aminoacids,
adding one to another, and the code automatically computes the
exact conformation of the sequence, following the desired options
on the secondary structure.