Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models

2010 ◽  
Vol 6 (2) ◽  
pp. 459-466 ◽  
Author(s):  
Pär Bjelkmar ◽  
Per Larsson ◽  
Michel A. Cuendet ◽  
Berk Hess ◽  
Erik Lindahl
Keyword(s):  
Force Field ◽  
Protein Stability ◽  
Interaction Sites ◽  
Virtual Interaction ◽  
Charmm Force Field ◽  
Water Models

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

Revised CHARMM force field parameters for iron-containing cofactors of photosystem II

2017 ◽  
Vol 39 (1) ◽  
pp. 7-20 ◽  
Author(s):  
Suliman Adam ◽  
Michaela Knapp-Mohammady ◽  
Jun Yi ◽  
Ana-Nicoleta Bondar
Keyword(s):  
Photosystem Ii ◽  
Force Field ◽  
Charmm Force Field ◽  
Force Field Parameters

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.

scholarly journals Modeling the effect of ion‐induced shock waves and DNA breakage with the reactive CHARMM force field

2020 ◽  
Vol 41 (28) ◽  
pp. 2429-2439
Author(s):  
Ida Friis ◽  
Alexey Verkhovtsev ◽  
Ilia A. Solov'yov ◽  
Andrey V. Solov'yov
Keyword(s):  
Shock Waves ◽  
Force Field ◽  
Dna Breakage ◽  
Charmm Force Field

Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models

2018 ◽  
Vol 58 (5) ◽  
pp. 1037-1052 ◽  
Author(s):  
Haiyang Zhang ◽  
Chunhua Yin ◽  
Yang Jiang ◽  
David van der Spoel
Keyword(s):  
Amino Acids ◽  
Force Field ◽  
Water Models ◽  
And Diffusion

scholarly journals CHARMM-DYES: Parameterization of Fluorescent Dyes for Use with the CHARMM Force Field

2020 ◽  
Vol 16 (12) ◽  
pp. 7817-7824
Author(s):  
Robert A. Shaw ◽  
Tristan Johnston-Wood ◽  
Benjamin Ambrose ◽  
Timothy D. Craggs ◽  
J. Grant Hill
Keyword(s):  
Force Field ◽  
Fluorescent Dyes ◽  
Charmm Force Field
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