Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-Bath dynamics and tests on model alpha-helical systems
Article Abstract:
A study introduces the Langevin dynamics with the united-residue (UNRES) force field to take into account the dynamic effects of the solvent. It is found that the UNRES time scale is 4 times longer than that of all-atom molecular dynamics simulations because the degrees of freedom corresponding to the fastest motions in UNRES are averaged out.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2005
User Contributions:
Comment about this article or add new information about this topic:
Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and test of the optimization method with single training proteins
Article Abstract:
Study is presented on the modification and parametrization of the united-residue (UNRES) force field for energy-based protein structure prediction and protein folding simulations. Result demonstrates that it is possible to optimize the UNRES force field for canonical simulations using a protein of any type of secondary structure.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2007
User Contributions:
Comment about this article or add new information about this topic:
Molecular dynamics with the united-residue force field: Ab initio folding simulations of multichain proteins
Article Abstract:
Molecular dynamics is implemented with united-residue (UNRES) force field to treat multichain proteins. Simulations are carried out for both isolated single chains and the multichain complexes.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2007
User Contributions:
Comment about this article or add new information about this topic:
- Abstracts: Molecular dynamics simulation of the structural and dynamic properties of dioctadecyldimethyl ammoniums in organoclays
- Abstracts: Molecular dynamics simulation of liquid water confined inside graphite channels: Dielectric and dynamical properties
- Abstracts: Molecular simulations of adsorption isotherms for linear and branched alkanes and their mixtures in silicalite
- Abstracts: Nucleation thermodynamics of cubic boron nitride upon high-pressure and high-temperature supercritical fluid system in nanoscale
- Abstracts: Molecular modeling of interactions between L-lysine and functionalized quartz surfaces. Molecular modeling of interactions between L-lysine and a hydroxylated quartz surface