(Q36960616)

17 August 2017

Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions (English)

1 reference

17 August 2017

1 reference

Simon Bernèche

0 references

Wojciech Wojtas-Niziurski

series ordinal

1 reference

17 August 2017

Yilin Meng

series ordinal

1 reference

17 August 2017

Benoit Roux

series ordinal

1 reference

17 August 2017

1 April 2013

1 reference

Journal of Chemical Theory and Computation

17 August 2017

1 reference

17 August 2017

1 reference

17 August 2017

1 reference

17 August 2017

1885-1895

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Convergence and error estimation in free energy calculations using the weighted histogram analysis method

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

CHARMM: the biomolecular simulation program

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Finding transition pathways using the string method with swarms of trajectories

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Scalable molecular dynamics with NAMD

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

A microscopic view of ion conduction through the K+ channel.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Escaping free-energy minima

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Canonical dynamics: Equilibrium phase-space distributions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Simultaneous escaping of explicit and hidden free energy barriers: application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Single-sweep methods for free energy calculations

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Adaptive biasing force method for scalar and vector free energy calculations

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

String method in collective variables: minimum free energy paths and isocommittor surfaces

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

On the potential functions used in molecular dynamics simulations of ion channels

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Energetics of ion conduction through the K+ channel

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Equilibrium Free Energies from Nonequilibrium Metadynamics

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694627

Assessing the Accuracy of Metadynamics†

4 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23814508

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The potassium permeability of a giant nerve fibre

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23814508

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Optimized Monte Carlo data analysis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23814508

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT300978B

1 reference

17 August 2017

1 reference

17 August 2017

PubMed publication ID

23814508

1 reference