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 CRS4 and are generated with the molecular graphics code GMC.

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 spectroscopic findings.

• 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 the 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.

(under construction)