Molecular dynamics simulation free energy calculations

Key Words molecular dynamics simulations, free energy calculations, sensitivity analysis, dynamic pharmacophore, relaxed complex method... 

D. M. Ferguson, G. L. Seibel, and P. A. Kollman, AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules, Comp. Phys. Comm. 91 1 (1995). 

D. Ferguson, G. Seibel, and P. Kollman, Comput. Phys. Commun., 91,1 (1995). AMBER, a Package of Computer Programs for Applying Molecular Mechanics, Normal Mode Analysis, Molecular Dynamics and Free Energy Calculations to Simulate the Structural and Energetic Properties of Molecules. 

Einally, we draw attention to several review articles in this area. In 1986 Lowdin 23 considered various aspects of the historical development of computational QC in view of the development of both conventional supercomputers and large-scale parallel computers. More recently, Weineri24 presented a discussion on the programming of parallel computers and their use in molecular dynamics simulations, free energy perturbation, and large scale ab initio calculations, as well as the use of very elaborate graphical display programs in chemistry research. We also note a review on the use of parallel processors in... 

As conformational sampling is the main bottleneck in the simulation process, efforts have been made to parallelize AMBER for use in both molecular dynamics and free energy calculations. A recent collaboration involving, in addition to AMBER authors, Mike Crowley of the Pittsburgh Supercomputer Center, has led to a very exciting parallel version of the program which enables each nanosecond simulation of a 40000 atom system, the thyroid hormone receptor, using PME electrostatics to be completed on 128 processor of the CRAY T3E in about half a week, about six times faster than the calculation would have taken on the previous version of the software, which was quite efficient on the CRAY T3D. 

Eds., Wiley-VCH, New York, 1998, Vol. 12, pp. 1-74. Calculation of the Free Energy and the Entropy of Macromolecular Systems by Computer Simulation. T. P. Ly brand, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1990, Vol. 1, pp. 295-320. Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods. 

Tel. 415-476-4637, fax 415-476-0688, e-mail pak cgl.ucsf.edu Assisted Model Building using Energy Refinement. Energy minimization, molecular dynamics, and free energy perturbation (FEP) calculations. SPASMS (San Francisco Package of Applications for the Simulation of Molecular Systems). VAX, Cray versions. 

Hermans, J., Yun, R. H., Anderson, A. G. Precision of free-energies calculated by molecular dynamics simulations of peptides in solution. J. Comp. Chem. 13 (1992) 429-442... 

Just as one may wish to specify the temperature in a molecular dynamics simulation, so may be desired to maintain the system at a constant pressure. This enables the behavior of the system to be explored as a function of the pressure, enabling one to study phenomer such as the onset of pressure-induced phase transitions. Many experimental measuremen are made under conditions of constant temperature and pressure, and so simulations in tl isothermal-isobaric ensemble are most directly relevant to experimental data. Certai structural rearrangements may be achieved more easily in an isobaric simulation than i a simulation at constant volume. Constant pressure conditions may also be importai when the number of particles in the system changes (as in some of the test particle methoc for calculating free energies and chemical potentials see Section 8.9). 

---