"At the end of the method, the results may be displayed on a screen or printout.
"To put the method into the context of the full simulation, a method of molecular simulation of a system over time can be provided, comprising:
"modelling the system using an atomistic model;
"carrying out the method of simulating behaviour of a thermodynamic system according to any of the preceding claims; and
"analysing the results obtained from the simulation and relating them to macroscopic level properties.
"Embodiments of another aspect of the invention provide an apparatus which simulates behaviour of a thermodynamic system over time, the thermodynamic system having potential energy that can be split into more quickly varying parts and more slowly varying parts and having a state described by collective vectors of position and momentum at any given time; the apparatus comprising: a momentum refreshment part operable to carry out an operation of mixing the collective momentum vector with a noise vector and an acceptance/rejection operation; a conservative dynamics part operable to apply a multiple time stepping conservative dynamics operation to a current state, in which operation calculations for forces corresponding to more slowly varying energy parts in the thermodynamic system undergo an averaging procedure and are carried out at a larger time step than calculations for forces corresponding to more quickly varying energy parts; and to carry out an acceptance/rejection operation; wherein the acceptance/rejection operations are based on an approximation of the system energy expressed using shadow Hamiltonians and comprise accepting a current state or returning a replacement state.
"The preferred features of the above method statements are also applicable to this apparatus aspect and to the following computer program aspect.
"In any of the above aspects, the various features may be implemented in hardware, or as software modules running on one or more processors.
"The method is preferably carried out by a computer or computer network, the specification and arrangement of such computing functionality being well known to a person skilled in the art of molecular simulation.
"The invention thus also provides a computer program or a computer program product for carrying out any of the methods described herein, and a computer readable medium having stored thereon a program for carrying out any of the methods described herein. A computer program embodying the invention may be stored on a computer-readable medium, or it could, for example, be in the form of a signal such as a downloadable data signal provided from an Internet website, or it could be in any other form.
"The present invention can be implemented to give many advantages over the prior art methods for simulating multi-scale systems, for example over a range of thermodynamic ensembles such as NPT and NVT ensembles.
"General features of the prior art and preferred features of the present invention will now be described, purely by way of example, with reference to the accompanying drawings, in which:
BRIEF DESCRIPTIONS OF THE DRAWING
"FIG. 1 depicts the dynamics of molecules such as protein molecules;
"FIG. 2 is a diagramatic explanation of the MTS idea;
"FIG. 3 is a flowchart showing a general embodiment of the invention;
"FIG. 4 is a graph of numerical H against effective outer step size for MTS-LD and MTS-GSHMC; and
"FIG. 5 is a graph of the autocorrelation functions of diatomic centre of mass velocities for MTS-GSHMC as a function of the outer time-step .DELTA.t."
For more information, see this patent: Akhmatskaya, Elena Vitalievna; Reich, Sebastian. Method, Apparatus and
Keywords for this news article include: Physics,
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