Molecular dynamics simulation has been extensively applied to analyses of structure, dynamics, and function of biological molecules. Various methods implemented in a newly developed software, PEACH (Program for Energetic Analysis of bioCHemical molecules), are described. This review covers: (1) an outline of classical molecular dynamics, (2) generation of the initial structure and temperature, (3) computation of force and potential, (4) time integration, (5) ensemble, and (6) analyses of the generated trajectories.
It has been recognized that most physical chemistry calculations are conveniently performed on desk top computers with a program code written in BASIC languages. The compilers for this purpose are considerably cheaper than FORTRAN ones. We have developed a program converter from FORTRAN 77 to F-BASIC(Fuji-tsuLtd.) on WINDOWS95/98 (Microsoft Corp.). It was confirmed that some short simple FORTRAN programs are converted with our method to give satisfactory results without any manual modification. These converted programs were able to run with some other BASIC environments such as Quick BASIC and N88-BASIC following some modifications.