[SMMP] A modern package for simulation of proteins Original Research Article

A Fortran package is presented which provides useful routines for molecular simulation of proteins within the standard geometry model. Highly efficient algorithms for the calculation of energy and its derivatives are implemented. A set of energy minimization routines and modern Monte Carlo algorithms are added. Three different parameter sets are used to calculate the internal energy: ECEPP/2 potential, ECEPP/3 and the FLEX potential. The solvation energy of the protein can be calculated using the solvent accessible area method. The program is fast and may be successfully exploited even on a single PC. The code is free and open, and can be easily modified. Hence, the package allows researchers and students in a simple and inexpensive way to become familiar with protein simulation techniques, and is especially suitable for lecturers teaching molecular simulation. Yet, when exploited on advanced computers or PC clusters, it is a powerful tool and also valuable for advanced researchers.