FENZI: GPU-Enabled Molecular Dynamics Simulations of Large Membrane Regions Based on the CHARMM Force Field and PME

2011 ◽  
Author(s):  
Narayan Ganesan ◽  
Michela Taufer ◽  
Brad Bauer ◽  
Sandeep Patel
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Charmm Force Field ◽  
Dynamics Simulations

scholarly journals New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations

RSC Advances ◽  
2014 ◽  
Vol 4 (89) ◽  
pp. 48621-48631 ◽  
Author(s):  
Eleanor R. Turpin ◽  
Sam Mulholland ◽  
Andrew M. Teale ◽  
Boyan B. Bonev ◽  
Jonathan D. Hirst
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Amino Acid Residues ◽  
Charmm Force Field ◽  
Force Field Parameters ◽  
Dynamics Simulations

scholarly journals Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins

2021 ◽  
Vol 23 (1) ◽  
pp. 473
Author(s):  
Olgun Guvench ◽  
Devon Martin ◽  
Megan Greene
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Biomolecular Dynamics ◽  
Explicit Solvent ◽  
Conformational Properties ◽  
Adaptive Biasing ◽  
Charmm Force Field ◽  
Ring Puckering ◽  
Dynamics Simulations

The conformational properties of carbohydrates can contribute to protein structure directly through covalent conjugation in the cases of glycoproteins and proteoglycans and indirectly in the case of transmembrane proteins embedded in glycolipid-containing bilayers. However, there continue to be significant challenges associated with experimental structural biology of such carbohydrate-containing systems. All-atom explicit-solvent molecular dynamics simulations provide a direct atomic resolution view of biomolecular dynamics and thermodynamics, but the accuracy of the results depends on the quality of the force field parametrization used in the simulations. A key determinant of the conformational properties of carbohydrates is ring puckering. Here, we applied extended system adaptive biasing force (eABF) all-atom explicit-solvent molecular dynamics simulations to characterize the ring puckering thermodynamics of the ten common pyranose monosaccharides found in vertebrate biology (as represented by the CHARMM carbohydrate force field). The results, along with those for idose, demonstrate that the CHARMM force field reliably models ring puckering across this diverse set of molecules, including accurately capturing the subtle balance between 4C1 and 1C4 chair conformations in the cases of iduronate and of idose. This suggests the broad applicability of the force field for accurate modeling of carbohydrate-containing vertebrate biomolecules such as glycoproteins, proteoglycans, and glycolipids.

Ab initio based force field and molecular dynamics simulations of crystalline TATB

2004 ◽  
Vol 120 (15) ◽  
pp. 7059-7066 ◽  
Author(s):  
Richard H. Gee ◽  
Szczepan Roszak ◽  
Krishnan Balasubramanian ◽  
Laurence E. Fried
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

scholarly journals First-Principles-Based Interatomic Potential for SI and Its Thermal Conductivity

2011 ◽  
Author(s):  
Keivan Esfarjani ◽  
Gang Chen ◽  
Asegun Henry
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Thermal Properties ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
First Principles ◽  
Density Functional ◽  
Interatomic Potential ◽  
Force Constants ◽  
Dynamics Simulations

Based on first-principles density-functional calculations, we have developed and tested a force-field for silicon, which can be used for molecular dynamics simulations and the calculation of its thermal properties. This force field uses the exact Taylor expansion of the total energy about the equilibrium positions up to 4th order. In this sense, it becomes systematically exact for small enough displacements, and can reproduce the thermodynamic properties of Si with high fidelity. Having the harmonic force constants, one can easily calculate the phonon spectrum of this system. The cubic force constants, on the other hand, will allow us to compute phonon lifetimes and scattering rates. Results on equilibrium Green-Kubo molecular dynamics simulations of thermal conductivity as well as an alternative calculation of the latter based on the relaxation-time approximation will be reported. The accuracy and ease of computation of the lattice thermal conductivity using these methods will be compared. This approach paves the way for the construction of accurate bulk interatomic potentials database, from which lattice dynamics and thermal properties can be calculated and used in larger scale simulation methods such as Monte Carlo.

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