scholarly journals gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations

2018 ◽  
Author(s):  
M. Eric Irrgang ◽  
Jennifer M. Hays ◽  
Peter M. Kasson
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Structures ◽  
Folding Kinetics ◽  
Conformational Ensembles ◽  
Simulation Engine ◽  
Dynamics Simulations ◽  
High Level ◽  
Abstract Interface ◽  
Simulation Package

AbstractSummaryMolecular dynamics simulations have found use in a wide variety of biomolecular applications, from protein folding kinetics to computational drug design to refinement of molecular structures. Two areas where users and developers frequently need to extend the built-in capabilities of most software packages are implementing custom interactions, for instance biases derived from experimental data, and running ensembles of simulations. We present a Python high-level interface for the popular simulation package GROMACS that 1) allows custom potential functions without modifying the simulation package code, 2) maintains the optimized performance of GROMACS, and 3) presents an abstract interface to building and executing computational graphs that allows transparent low-level optimization of data flow and task placement. Minimal dependencies make this integrated API for the GROMACS simulation engine simple, portable, and maintainable. We demonstrate this API for experimentally-driven refinement of protein conformational ensembles.AvailabilitySource and installation instructions are available at https://github.com/kassonlab/gmxapi.

scholarly journals Short Pyridine-Furan Springs Exhibit Bistable Dynamics of Duffing Oscillators

Nanomaterials ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3264
Author(s):  
Vladik A. Avetisov ◽  
Maria A. Frolkina ◽  
Anastasia A. Markina ◽  
Alexander D. Muratov ◽  
Vladislav S. Petrovskii
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Stochastic Resonance ◽  
Duffing Oscillator ◽  
Molecular Structures ◽  
Thermally Activated ◽  
Responsive Polymers ◽  
Bistable Dynamics ◽  
Dynamics Simulations ◽  
Intensive Development

The intensive development of nanodevices acting as two-state systems has motivated the search for nanoscale molecular structures whose dynamics are similar to those of bistable mechanical systems, such as Euler arches and Duffing oscillators. Of particular interest are the molecular structures capable of spontaneous vibrations and stochastic resonance. Recently, oligomeric molecules that were a few nanometers in size and exhibited the bistable dynamics of an Euler arch were identified through molecular dynamics simulations of short fragments of thermo-responsive polymers subject to force loading. In this article, we present molecular dynamics simulations of short pyridine-furan springs a few nanometers in size and demonstrated the bistable dynamics of a Duffing oscillator with thermally-activated spontaneous vibrations and stochastic resonance.

scholarly journals Making connections between ultrafast protein folding kinetics and molecular dynamics simulations

2011 ◽  
Vol 108 (15) ◽  
pp. 6103-6108 ◽  
Author(s):  
T. Cellmer ◽  
M. Buscaglia ◽  
E. R. Henry ◽  
J. Hofrichter ◽  
W. A. Eaton
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Molecular Dynamics Simulations ◽  
Folding Kinetics ◽  
Dynamics Simulations

The cubyl cation rearrangements

2016 ◽  
Vol 52 (16) ◽  
pp. 3403-3405 ◽  
Author(s):  
Said Jalife ◽  
Sukanta Mondal ◽  
Jose Luis Cabellos ◽  
Gerardo Martinez-Guajardo ◽  
Maria A. Fernandez-Herrera ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Dynamics Simulations ◽  
High Level

Born–Oppenheimer molecular dynamics simulations and high-level ab initio computations predict that the cage-opening rearrangement of the cubyl cation to the 7H+-pentalenyl cation is feasible in the gas phase.

scholarly journals Explicit-pH Coarse-Grained Molecular Dynamics Simulations Enable Insights into Restructuring of Intestinal Colloidal Aggregates with Permeation Enhancers

Processes ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 29
Author(s):  
Shakhawath Hossain ◽  
Albin Parrow ◽  
Aleksei Kabedev ◽  
Rosita Carolina Kneiszl ◽  
Yuning Leng ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ph Dependence ◽  
Molecular Structures ◽  
Aggregation Behavior ◽  
Coarse Grained ◽  
Permeation Enhancers ◽  
Fed State ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

Permeation enhancers (PEs) can increase the bioavailability of drugs. The mechanisms of action of these PEs are complex, but, typically, when used for oral administration, they can transiently induce the alteration of trans- and paracellular pathways, including increased solubilization and membrane fluidity, or the opening of the tight junctions. To elucidate these mechanistic details, it is important to understand the aggregation behavior of not only the PEs themselves but also other molecules already present in the intestine. Aggregation processes depend critically on, among other factors, the charge state of ionizable chemical groups, which is affected by the pH of the system. In this study, we used explicit-pH coarse-grained molecular dynamics simulations to investigate the aggregation behavior and pH dependence of two commonly used PEs—caprate and SNAC—together with other components of fasted- and fed-state simulated intestinal fluids. We also present and validate a coarse-grained molecular topology for the bile salt taurocholate suitable for the Martini3 force-field. Our results indicate an increase in the number of free molecules as a function of the system pH and for each combination of FaSSIF/FeSSIF and PEs. In addition, there are differences between caprate and SNAC, which are rationalized based on their different molecular structures and critical micelle concentrations.

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