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Implementation of replica-exchange umbrella sampling in GAMESS

Journal Article · · Computer Physics Communications
 [1];  [2];  [1];  [1]
  1. Nagoya Univ. (Japan)
  2. National Inst. of Advanced Industrial Science and Technology (AIST), Tsukuba (Japan)
+ Show Author Affiliations

In GAMESS-US quantum chemistry package, both replica-exchange molecular dynamics (REMD) and the umbrella sampling (US) methods are available. However, prior to this work, the replica-exchange umbrella sampling (REUS) method, combining REMD and US, was not implemented. Here, REUS affords a more efficient conformational sampling than the conventional US method and is often used in MD simulations. We implemented REUS in GAMESS-US and improved some routines of the existing REMD code. A density-functional tight-binding REMD (DFTB-REMD) simulation of alanine deca-peptide and a DFTB-MD REUS simulation of proton transfer in malonaldehyde were performed. The results of DFTB-MD REUS simulations performed with three different simulation packages were compared to validate our GAMESS-US implementation.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE; Japan Society for the Promotion of Science (JSPS)
Grant/Contract Number:
AC05-00OR22725
OSTI ID:
1659568
Journal Information:
Computer Physics Communications, Journal Name: Computer Physics Communications Journal Issue: 1 Vol. 228; ISSN 0010-4655
Publisher:
ElsevierCopyright Statement
Country of Publication:
United States
Language:
English

References (52)

Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram journal October 2001
Unraveling the Stability of Polypeptide Helices: Critical Role of van der Waals Interactions journal March 2011
Quantum Chemical Molecular Dynamics Model Study of Fullerene Formation from Open-Ended Carbon Nanotubes † journal April 2004
Towards an Understanding of Channelrhodopsin Function: Simulations Lead to Novel Insights of the Channel Mechanism journal May 2013
Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties journal September 1998
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling journal February 1977
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations journal July 1983
Generalized-ensemble algorithms for molecular simulations of biopolymers journal January 2001
The calculation of the potential of mean force using computer simulations journal September 1995
Molecular dynamics and Monte Carlo simulations favor the .alpha.-helical form for alanine-based peptides in water journal December 1993
Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States journal March 2001
From C 2 Molecules to Self-Assembled Fullerenes in Quantum Chemical Molecular Dynamics journal December 2003
Implementation of replica-exchange umbrella sampling in the DFTB + semiempirical quantum chemistry package journal July 2016
Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations journal February 2013
Constant-temperature free energy surfaces for physical and chemical processes journal April 1993
Nosé–Hoover chains: The canonical ensemble via continuous dynamics journal August 1992
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers journal September 2015
Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model journal June 1985
Inhomogeneous Electron Gas journal November 1964
Wave Functions for Impurity Levels journal September 1954
Exchange Monte Carlo Method and Application to Spin Glass Simulations journal June 1996
DFT studies on helix formation in N-acetyl-(L-alanyl)n-N′-methylamide for n=1–20 journal May 2000
Efficient Parallel Implementations of QM/MM-REMD (Quantum Mechanical/Molecular Mechanics-Replica-Exchange MD) and Umbrella Sampling: Isomerization of H 2 O 2 in Aqueous Solution journal June 2013
A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method journal January 2001
THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method journal October 1992
VMD: Visual molecular dynamics journal February 1996
Brownian dynamics: Its application to ionic solutions journal April 1977
New Monte Carlo algorithms for protein folding journal April 1999
Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry journal July 2015
Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations journal May 2004
Replica-exchange molecular dynamics method for protein folding journal November 1999
Ab initio quantum mechanical models of peptide helices and their vibrational spectra journal August 2002
Replica-Exchange Molecular Dynamics Simulations for Various Constant Temperature Algorithms journal July 2010
DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB) journal March 2011
A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO) journal January 2004
Simulation of the (H2O)8 cluster with the SCC-DFTB electronic structure method journal August 2012
Self-Consistent Equations Including Exchange and Correlation Effects journal November 1965
Fragment molecular orbital method: an approximate computational method for large molecules journal November 1999
Simulated Tempering: A New Monte Carlo Scheme journal July 1992
Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models journal September 2014
Multidimensional replica-exchange method for free-energy calculations journal October 2000
DFTB+, a Sparse Matrix-Based Implementation of the DFTB Method † journal July 2007
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu journal April 2010
QM/MM free energy simulations: recent progress and challenges journal July 2016
Note on an Approximation Treatment for Many-Electron Systems journal October 1934
The Wave Mechanics of an Atom with a non-Coulomb Central Field. Part III. Term Values and Intensities in Series in Optical Spectra journal July 1928
Ab initio replica-exchange Monte Carlo method for cluster studies journal January 2001
Multicanonical ensemble: A new approach to simulate first-order phase transitions journal January 1992
General atomic and molecular electronic structure system journal November 1993
New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles journal February 1992
N�herungsmethode zur L�sung des quantenmechanischen Mehrk�rperproblems journal January 1930
Multicanonical algorithms for first order phase transitions journal September 1991

Cited By (1)

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97 MATHEMATICS AND COMPUTING
density-functional tight-binding
GAMESS-US
multidimensional replica-exchange method
replica-exchange molecular dynamics
replica-exchange umbrella sampling
umbrella sampling