Calculation of the entropy and free energy from monte carlo simulations of a peptide stretched by an external force.
Hypothetical scanning Monte Carlo (HSMC) is a method for calculating the absolute entropy, S, and free energy, F, from a trajectory generated by any simulation technique. HSMC was applied initially to fluids (argon and water) and later to peptides and self-avoiding walks on a lattice. In this paper we make a step further and apply it to a model of decaglycine (at T = 300 K) in vacuum with constant bond lengths where external stretching forces are exerted at the end points; the changes in S and F are calculated as the forces are increased. The molecule is placed initially in a helical structure, which is changed to an extended structure after a short simulation time due to the exerted forces. This study has relevance to problems in polymers (e.g., rubber elasticity) and to the analysis of experiments where individual molecules are stretched by atomic force microscopy (AFM), for example. The results for S and F are accurate and are significantly better than those obtained by the quasi-harmonic approximation and the local states method. However, the molecule is quite stiff due to the strong bond angle potentials and the extensions are small even for relatively large forces. Correspondingly, as the force is increased the decrease in the entropy is relatively small while the potential energy is enhanced significantly. Still, differences, TDeltaS, for different forces are obtained with very good accuracy of approximately 0.2 kcal/mol.
Cheluvaraja
Srinath
S
Department of Computational Biology, University of Pittsburgh School of Medicine, W1058 BST, Pittsburgh, Pennsylvania 15261, USA.
Meirovitch
Hagai
H
D003198:Computer Simulation; D019277:Entropy; D008956:Models, Chemical; D009010:Monte Carlo Method; D009842:Oligopeptides / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D013314:Stress, Mechanical; D013816:Thermodynamics
D009842:Oligopeptides; D010455:Peptides; C070361:decaglycine