scholarly journals Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization

2016 ◽  
Vol 120 (33) ◽  
pp. 8217-8229 ◽  
Author(s):  
Mark S. Miller ◽  
Wesley K. Lay ◽  
Adrian H. Elcock
Keyword(s):  
Amino Acids ◽  
Force Field ◽  
Osmotic Pressure ◽  
Force Field Parameterization

Additive CHARMM36 Force Field for Nonstandard Amino Acids

2021 ◽  
Author(s):  
Anastasia Croitoru ◽  
Sang-Jun Park ◽  
Anmol Kumar ◽  
Jumin Lee ◽  
Wonpil Im ◽  
...  
Keyword(s):  
Amino Acids ◽  
Force Field

scholarly journals Adsorption of Amino Acids on Graphene: Assessment of Current Force Fields

2019 ◽  
Author(s):  
Siva Dasetty ◽  
John K. Barrows ◽  
Sapna Sarupria
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Force Field ◽  
Force Fields ◽  
Principal Component ◽  
Free Energies ◽  
Adsorbed State ◽  
Free Energy Of Adsorption ◽  
Density Based Clustering ◽  
Structural Preferences

<div> <div> <div> <p>We compare the free energies of adsorption (∆Aads) and the structural preferences of amino acids obtained using the force fields — Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid–graphene interactions are favorable irrespective of the force field. While the magnitudes of ∆Aads differ between the force fields, the trends in the free energy of adsorption with amino acids are similar across the studied force fields. ∆Aads positively correlates with amino acid–graphene and negatively correlates with graphene–water interaction energies. Using a combination of principal component analysis and density-based clustering technique, we grouped the structures observed in the graphene adsorbed state. The resulting population of clusters, and the conformation in each cluster indicate that the structures of the amino acid in the graphene adsorbed state vary across force fields. The differences in the conformations of amino acids are more severe in the graphene adsorbed state compared to the bulk state for all the force fields. Our findings suggest that while the thermodynamics of adsorption of proteins and peptides would be described consistently across different force fields, the structural preferences of peptides and proteins on graphene will be force field dependent. </p> </div> </div> </div>

scholarly journals Infinite Dilution Activity Coefficients as Constraints for Force Field Parameterization and Method Development

2018 ◽  
Author(s):  
Guilherme Duarte Ramos Matos ◽  
Gaetano Calabró ◽  
David Mobley
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Activity Coefficients ◽  
Infinite Dilution ◽  
Method Development ◽  
Molecular Design ◽  
Pearson Correlation ◽  
Free Energy Calculations ◽  
Infinite Dilution Activity Coefficients ◽  
Force Field Parameterization

<p>Molecular simulations see widespread use in calculating various physical properties of interest, with a key goal being predictive molecular design. These simulations, including molecular dynamics (MD) simulations, begin with a underlying energy model or force field and then, based on this model, use simulations to compute properties of interest. However, one of the most significant challenges in molecular dynamics and modeling studies is ensuring that the force field is a good enough approximation of the underlying physics that computed quantities can be used to reproduce experimental properties with the desired level of accuracy. Parameterization of force fields depend on various experimental properties including as much of the chemistry of interest as possible. Physicochemical properties measurable in a relatively straightforward manner are particularly interesting for developers. Such properties can be measured for a relatively diverse chemical set and used to expand the parameterization dataset as needed. Here, we examine infinite dilution activity coefficients (IDACs) which are experimental quantities that can play this role. We retrieved 237 empirical IDACs from NIST's ThermoML, a database of measured thermodynamic properties, and we estimated the corresponding values using solvation free energy calculations. We found that calculated IDAC values correlate strongly with experiment. Specifically, the natural logarithm of calculated and experimental IDAC values shows a Pearson correlation coefficient of 0.85+/-0.02. The calculated IDAC values allow us to identify strengths and potential weaknesses of force field parameters for specific functional groups in solutes and solvents, suggesting these may be a valuable source of data for force field parameterization, capturing some of the same type of information as hydration and solvation free energies and thus potentially providing a useful new source of experimental data.</p>

Force field parameterization for the 4-fluorophenyl group

1989 ◽  
Vol 10 (5) ◽  
pp. 711-717 ◽  
Author(s):  
D. H. Gregory ◽  
J. T. Gerig
Keyword(s):  
Force Field ◽  
Force Field Parameterization

scholarly journals How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

2011 ◽  
Vol 100 (9) ◽  
pp. L47-L49 ◽  
Author(s):  
Stefano Piana ◽  
Kresten Lindorff-Larsen ◽  
David E. Shaw
Keyword(s):  
Protein Folding ◽  
Force Field ◽  
Force Field Parameterization ◽  
Folding Simulations

Force-field parameterization of the galactic cosmic ray spectrum: Validation for Forbush decreases

2015 ◽  
Vol 55 (12) ◽  
pp. 2940-2945 ◽  
Author(s):  
I.G. Usoskin ◽  
G.A. Kovaltsov ◽  
O. Adriani ◽  
G.C. Barbarino ◽  
G.A. Bazilevskaya ◽  
...  
Keyword(s):  
Force Field ◽  
Cosmic Ray ◽  
Forbush Decreases ◽  
Force Field Parameterization ◽  
Galactic Cosmic Ray
Sign in / Sign up

Export Citation Format

Share Document