Integrated library-based growth and Monte Carlo simulations allow for improved sampling and free energy measurements
نویسندگان
چکیده
We have combined and integrated our previously developed librarybased Growth and Monte Carlo simulation techniques in order to allow for both thorough sampling and free energy measurements of all-atom peptides. The integrated growth and relaxation technique makes use of pre-calculated Boltzmann distributed statistical libraries of molecularfragments and their corresponding energies. Due to this new implementation, we are now able to accurately determine free energies and sample phase space for larger systems that were previously unattainable with library-based growth. We report sampling quality and statistics on free energy measurements for four polypeptide systems that we examined. We discuss possible applications of this new and more general library-based method.
منابع مشابه
Energy study at different solvents for potassium Channel Protein by Monte Carlo, Molecular and Langevin Dynamics Simulations
Potassium Channels allow potassium flux and are essential for the generation of electric current acrossexcitable membranes. Potassium Channels are also the targets of various intracellular controlmechanisms; such that the suboptimal regulation of channel function might be related to pathologicalconditions. Realistic studies of ion current in biologic channels present a major challenge for compu...
متن کاملGyration Radius and Energy Study at Different Temperatures for Acetylcholine Receptor Protein in Gas Phase by Monte Carlo, Molecular and Langevin Dynamics Simulations
The determination of gyration radius is a strong research for configuration of a Macromolecule. Italso reflects molecular compactness shape. In this work, to characterize the behavior of theprotein, we observe quantities such as the radius of gyration and the average energy. We studiedthe changes of these factors as a function of temperature for Acetylcholine receptor protein in gasphase with n...
متن کاملExtending fragment-based free energy calculations with library monte carlo simulation: Annealing in interaction space
Pre-calculated libraries of molecular fragment configurations have previously been used as a basis for both equilibrium sampling (via library-based Monte Carlo) and for obtaining absolute free energies using a polymer-growth formalism. Here, we combine the two approaches to extend the size of systems for which free energies can be calculated. We study a series of all-atom poly-alanine systems i...
متن کاملEnergy Study at Different Temperatures for Active Site of Azurin in Water, Ethanol, Methanol and Gas Phase by Monte Carlo Simulations
The interaction between the solute and the solsent molecules play a crucial role in understanding the various molecular processes involved in chemistry and biochemistry, so in this work the potential energy of active site of azurin have been calculated in solvent by the Monte Carlo simulation. In this paper we present quantitative results of Monte Carlo calculations of potential energies of ...
متن کاملA Monte Carlo simulation study of vinblastine and vincristine as clinical drugs
In this study, Monte Carlo statistical mechanical simulations for vinblastine and vincristine werecarried out in standard manner using the Metropolis sampling technique in canonical (T, V, N)ensemble., Geometrical optimizations of vinblastine and vincristine were carried out with the HFmethod coupled to 6-31G(d) basis sets for all atoms. Simulation was done by four force fields ofMM+, BIO+, AMB...
متن کامل