منابع مشابه
Force fields and molecular dynamics simulations
The objective of this review is to serve as an introductory guide for the non-expert to the exciting field of Molecular Dynamics (MD). MD simulations generate a phase space trajectory by integrating the classical equations of motion for a system of N particles. Here I review the basic concepts needed to understand the technique, what are the key elements to perform a simulation and which is the...
متن کاملDeveloping accurate molecular mechanics force fields for conjugated molecular systems.
A rapid method to parameterize the intramolecular component of classical force fields for complex conjugated molecules is proposed. The method is based on a procedure of force matching with a reference electronic structure calculation. It is particularly suitable for those applications where molecular dynamics simulations are used to generate structures that are therefore analysed by electronic...
متن کاملMachine learning of accurate energy-conserving molecular force fields
Using conservation of energy-a fundamental property of closed classical and quantum mechanical systems-we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of int...
متن کاملConstructing ab initio force fields for molecular dynamics simulations
We explore and discuss several important issues concerning the derivation of many-body force fields from ab initio quantum chemical data. In particular, we seek a general methodology for constructing ab initio force fields that are ‘‘chemically accurate’’ and are computationally efficient for large-scale molecular dynamics simulations. We investigate two approaches for modeling many-body intera...
متن کاملModern protein force fields behave comparably in molecular dynamics simulations
Several molecular dynamics simulations were performed on three proteins--bovine apo-calbindin D9K, human interleukin-4 R88Q mutant, and domain IIA of bacillus subtilis glucose permease--with each of the AMBER94, CHARMM22, and OPLS-AA force fields as implemented in CHARMM. Structural and dynamic properties such as solvent-accessible surface area, radius of gyration, deviation from their respecti...
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ژورنال
عنوان ژورنال: Nature
سال: 1940
ISSN: 0028-0836,1476-4687
DOI: 10.1038/146747d0