Development of Cu2+-Based Distance Methods and Force Field Parameters for the Determination of PNA Conformations and Dynamics by EPR and MD Simulations

2020 ◽  
Vol 124 (35) ◽  
pp. 7544-7556
Author(s):  
Austin Gamble Jarvi ◽  
Artur Sargun ◽  
Xiaowei Bogetti ◽  
Junmei Wang ◽  
Catalina Achim ◽  
...  
Keyword(s):  
Force Field ◽  
Md Simulations ◽  
Distance Methods ◽  
Force Field Parameters

Development of a computer program for the determination of force field parameters derived from ab initio pes

1995 ◽  
Author(s):  
Ugo Cosentino ◽  
Giorgio Moro ◽  
Demetrio Pitea ◽  
Mercedes Procopio ◽  
Pier Carlo Fantucci
Keyword(s):  
Computer Program ◽  
Force Field ◽  
Ab Initio ◽  
Force Field Parameters

Uncertainty Quantification in MD Simulations. Part II: Bayesian Inference of Force-Field Parameters

2012 ◽  
Vol 10 (4) ◽  
pp. 1460-1492 ◽  
Author(s):  
F. Rizzi ◽  
H. N. Najm ◽  
B. J. Debusschere ◽  
K. Sargsyan ◽  
M. Salloum ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Force Field ◽  
Uncertainty Quantification ◽  
Md Simulations ◽  
Force Field Parameters

scholarly journals Intermolecular Force Field Parameters Optimization for Computer Simulations of CH4in ZIF-8

2016 ◽  
Vol 2016 ◽  
pp. 1-6
Author(s):  
Phannika Kanthima ◽  
Pikul Puphasuk ◽  
Tawun Remsungnen
Keyword(s):  
Force Field ◽  
Md Simulations ◽  
Binding Energies ◽  
Parameters Optimization ◽  
Interaction Energies ◽  
Intermolecular Force ◽  
Amber Force Field ◽  
De Algorithm ◽  
Force Field Parameters ◽  
Structural Behaviors

The differential evolution (DE) algorithm is applied for obtaining the optimized intermolecular interaction parameters between CH4and 2-methylimidazolate ([C4N2H5]−) using quantum binding energies of CH4-[C4N2H5]−complexes. The initial parameters and their upper/lower bounds are obtained from the general AMBER force field. The DE optimized and the AMBER parameters are then used in the molecular dynamics (MD) simulations of CH4molecules in the frameworks of ZIF-8. The results show that the DE parameters are better for representing the quantum interaction energies than the AMBER parameters. The dynamical and structural behaviors obtained from MD simulations with both sets of parameters are also of notable differences.

Optimal determination of force field parameters for reduced molecular dynamics model

2019 ◽  
Vol 236 ◽  
pp. 86-94
Author(s):  
Hyun-Seok Kim ◽  
Jae-Hyun Kim ◽  
Song-Hyun Cha ◽  
Seonho Cho
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Dynamics Model ◽  
Force Field Parameters

scholarly journals An ab-initio study of pyrrole and imidazole arylamides

2013 ◽  
Vol 78 (11) ◽  
pp. 1789-1795
Author(s):  
Ara Abramyan ◽  
Zhiwei Liu ◽  
Vojislava Pophristic
Keyword(s):  
Dna Binding ◽  
Force Field ◽  
Dna Sequences ◽  
Density Functional ◽  
Md Simulations ◽  
Building Blocks ◽  
Amide Bond ◽  
Amide Bonds ◽  
Force Field Parameters ◽  
Arylamide Foldamers

Arylamide foldamers have been shown to have a number of biological and medicinal applications. For example, a class of pyrrole-imidazole polyamide foldamers is capable of binding specific DNA sequences and preventing development of various gene disorders, most importantly cancer. Molecular dynamics (MD) simulations can provide crucial details in understanding the atomic level events related to foldamer/DNA binding. An important first step in the accurate simulation of these foldamer/DNA systems is the reparametrization of force field parameters for torsion around the aryl-amide bonds. Here we highlight our Density Functional Theory (DFT) potential energy profiles and derived force field parameters for four aryl-amide bond types for the pyrrole and imidazole building blocks extensively used in foldamer design for the DNA-binding polyamides. These results contribute to developing of computational tools for an appropriate molecular modeling of pyrrole-imidazole polyamide/DNA binding, and provide an insight into the chemical factors that influence the flexibility of the pyrrole-imidazole polyamides, and their binding to DNA.

The determination of CHARMM force field parameters for the Mg2+ containing HIV-1 integrase

2018 ◽  
Vol 711 ◽  
pp. 1-7 ◽  
Author(s):  
Thommas Musyoka ◽  
Özlem Tastan Bishop ◽  
Kevin Lobb ◽  
Vuyani Moses
Keyword(s):  
Force Field ◽  
Charmm Force Field ◽  
Force Field Parameters ◽  
Hiv 1

Determination of approximate force field parameters

1989 ◽  
Vol 13 (2) ◽  
pp. 123-128 ◽  
Author(s):  
Markus Breuer ◽  
Gerhard Hägele
Keyword(s):  
Force Field ◽  
Force Field Parameters

Determination of AMBER Force Field Parameters for Thioester by Quantum Chemical Calculations

2013 ◽  
Vol 42 (10) ◽  
pp. 1206-1208 ◽  
Author(s):  
Akifumi Oda ◽  
Shuichi Fukuyoshi ◽  
Ryoichi Nakagaki ◽  
Ohgi Takahashi
Keyword(s):  
Force Field ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Amber Force Field ◽  
Force Field Parameters
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