Proteins and other peptides are aminoacid chains that perform specific biological functions within an organism. The functionality of these structures depends on their three-dimensional organization, so it is important to determine what are the factors that control the proper folding. If the sequence is known, in principle it would be possible to predict its 3D structure by means of molecular dynamics of all atoms of the sequence and the surrounding water molecules, but it is clear that this type of simulation is not feasible with the current computational resources. Alternatively, we consider simplified models that take into account only the main characteristics of each monomer and the particles of the medium. We have performed molecular dynamics simulations, considering the LennardJones-like interactions between monomers (distinguishing between polar and hydrophobic monomers) and additionally incorporating a stochastic (Langevin) force to complement the influence of the aqueous medium. We considered several linear sequences, symmetric, with fixed-length, evolving in the tri or bi-dimensional space. As a result of these simulations, we can describe the temporal evolution in the space of conformations through effective variables or reaction coordinates, such as gyration radius, distance between ends or number of contacts between unbound monomers. From the analysis of the time series of the effective variables, we extract the coefficients that allow to build the stochastic differential equation of motion of the effective variables or its associated Fokker-Planck equation. These equations for a limited number of degrees of freedom provide, in principle, information on conformational changes, which are difficult to access in the description of the original, high dimensional, phase. We discuss the advantages and limitations of this approach.