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Amirali Kia & Eric Darve. (2013) The accuracy of the CHARMM22/CMAP and AMBER ff99SB force fields for modelling the antimicrobial peptide cecropin P1. Molecular Simulation 39:11, pages 922-936.
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JÜRGEN SCHLITTER & MARCO KLÄHN. (2003) The free energy of a reaction coordinate at multiple constraints: a concise formulation. Molecular Physics 101:23-24, pages 3439-3443.
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IVAN COLUZZA, MICHIEL SPRIK & GIOVANNI CICCOTTI. (2003) Constrained reaction coordinate dynamics for systems with constraints. Molecular Physics 101:18, pages 2885-2894.
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Articles from other publishers (50)
Francisco Ospina-Acevedo, Luis A. Albiter, Kathleen O. Bailey, José Fernando Godínez-Salomón, Christopher P. Rhodes & Perla B. Balbuena. (2024)
Catalytic Activity and Electrochemical Stability of Ru
1–
x
M
x
O
2
(M = Zr, Nb, Ta): Computational and Experimental Study of the Oxygen Evolution Reaction
. ACS Applied Materials & Interfaces 16:13, pages 16373-16398.
Crossref
Crossref
Qinghua Li, Hongyu Wu, Menglong Sheng, Zhi Wang & Jixiao Wang. (2024) Analysis of the effect of amino density and water on amino-containing fixed carrier membranes via computational chemistry. Journal of Membrane Science 695, pages 122460.
Crossref
Crossref
Qingteng Chen, Jian Liu & Bo Yang. (2024) Microenvironment of the HMOR catalyst leads to high ethylene selectivity from ketene conversion: Insights from ab initio molecular dynamics simulations. Chemical Engineering Journal 481, pages 148412.
Crossref
Crossref
Saul Perez-Beltran, Wasif ZaheerZeyang Sun, William F. Defliese, Sarbajit Banerjee & Ethan L. Grossman. (2023) Density functional theory and ab initio molecular dynamics reveal atomistic mechanisms for carbonate clumped isotope reordering. Science Advances 9:26.
Crossref
Crossref
John Mark P. Martirez & Emily A. Carter. (2023) Solvent Dynamics Are Critical to Understanding Carbon Dioxide Dissolution and Hydration in Water. Journal of the American Chemical Society 145:23, pages 12561-12575.
Crossref
Crossref
Jose Fernando Godínez-Salomón, Francisco Ospina-Acevedo, Luis A. Albiter, Kathleen O. Bailey, Zachary G. Naymik, Rubén Mendoza-Cruz, Perla B. Balbuena & Christopher P. Rhodes. (2022) Titanium Substitution Effects on the Structure, Activity, and Stability of Nanoscale Ruthenium Oxide Oxygen Evolution Electrocatalysts: Experimental and Computational Study. ACS Applied Nano Materials 5:8, pages 11752-11775.
Crossref
Crossref
Luke J. Wirth, Christopher Woodward & Amir A. Farajian. (2022) Ab initio molecular dynamics of pipe diffusion in fcc Ni beyond transition state theory. Acta Materialia 222, pages 117357.
Crossref
Crossref
Maria M. Reif & Martin Zacharias. 2022. Computational Methods for Estimating the Kinetic Parameters of Biological Systems. Computational Methods for Estimating the Kinetic Parameters of Biological Systems
255
292
.
Qingteng Chen, Jian Liu & Bo Yang. (2021) Identifying the key steps determining the selectivity of toluene methylation with methanol over HZSM-5. Nature Communications 12:1.
Crossref
Crossref
Chao Peng, Jianfu Chen, Peijun Hu & Haifeng Wang. (2021) Molecular Adsorption Kinetics: Nonlinear Entropy–Enthalpy Loss Quantified by Constrained AIMD and Insights into the Adsorption-Site Determination on Metal Oxides. The Journal of Physical Chemistry C 125:20, pages 10974-10982.
Crossref
Crossref
Jun-Ping Du, W. T. Geng, Kazuto Arakawa, Ju Li & Shigenobu Ogata. (2020) Hydrogen-Enhanced Vacancy Diffusion in Metals. The Journal of Physical Chemistry Letters 11:17, pages 7015-7020.
Crossref
Crossref
Huong T.T. Ta, A. Kiet Tieu, Hongtao Zhu, Haibo Yu, Nam V. Tran, Bach H. Tran, Shanhong Wan & Thi D. Ta. (2020) Ab initio study on physical and chemical interactions at borates and iron oxide interface at high temperature. Chemical Physics 529, pages 110548.
Crossref
Crossref
Junfeng Gao, Gang Zhang, Boris I. Yakobson & Yong-Wei Zhang. (2018) Kinetic theory for the formation of diamond nanothreads with desired configurations: a strain–temperature controlled phase diagram. Nanoscale 10:20, pages 9664-9672.
Crossref
Crossref
Tomáš Bučko, Siwar Chibani, Jean-François Paul, Laurent Cantrel & Michael Badawi. (2017) Dissociative iodomethane adsorption on Ag-MOR and the formation of AgI clusters: an ab initio molecular dynamics study. Phys. Chem. Chem. Phys. 19:40, pages 27530-27543.
Crossref
Crossref
Tomáš Bučko & Jürgen Hafner. (2015) The role of spatial constraints and entropy in the adsorption and transformation of hydrocarbons catalyzed by zeolites. Journal of Catalysis 329, pages 32-48.
Crossref
Crossref
Gerhard König & Bernard R. Brooks. (2015) Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations. Biochimica et Biophysica Acta (BBA) - General Subjects 1850:5, pages 932-943.
Crossref
Crossref
Olga N. Samoylova, Emvia I. Calixte & Kevin L. Shuford. (2015) Molecular Dynamics Simulations of Ion Transport in Carbon Nanotube Channels. The Journal of Physical Chemistry C 119:4, pages 1659-1666.
Crossref
Crossref
Peng Tao, Alexander J. Sodt, Yihan Shao, Gerhard König & Bernard R. Brooks. (2014) Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics. Journal of Chemical Theory and Computation 10:10, pages 4198-4207.
Crossref
Crossref
Andreas Vitalis & Rohit V. Pappu. (2014) A simple molecular mechanics integrator in mixed rigid body and dihedral angle space. The Journal of Chemical Physics 141:3.
Crossref
Crossref
Wouter K. den Otter. (2013) Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile. Journal of Chemical Theory and Computation 9:9, pages 3861-3865.
Crossref
Crossref
Caroline Mellot-Draznieks, Vassili Valayannopoulos, Dominique Chrétien, Arnold Munnich, Pascale de Lonlay & Hervé Toulhoat. (2012) Relative Enzymatic Activity Levels from In Silico Mutagenesis.. ACS Catalysis 2:12, pages 2673-2686.
Crossref
Crossref
Jieqiong Lin, Brian Novak & Dorel Moldovan. (2012) Molecular Dynamics Simulation Study of the Effect of DMSO on Structural and Permeation Properties of DMPC Lipid Bilayers. The Journal of Physical Chemistry B 116:4, pages 1299-1308.
Crossref
Crossref
J. Schlitter. (2011) Constraint methods for determining pathways and free energy of activated processes. The European Physical Journal Special Topics 200:1, pages 91-105.
Crossref
Crossref
P. Echenique, C. N. Cavasotto & P. García-Risueño. (2011) The canonical equilibrium of constrained molecular models. The European Physical Journal Special Topics 200:1, pages 5-54.
Crossref
Crossref
Tomáš Bučko, Lubomir Benco, Jürgen Hafner & János G. Ángyán. (2011) Monomolecular cracking of propane over acidic chabazite: An ab initio molecular dynamics and transition path sampling study. Journal of Catalysis 279:1, pages 220-228.
Crossref
Crossref
T Bucko & J Hafner. (2010) Entropy effects in hydrocarbon conversion reactions: free-energy integrations and transition-path sampling. Journal of Physics: Condensed Matter 22:38, pages 384201.
Crossref
Crossref
Wouter K. den Otter. (2009) Free energies of stable and metastable pores in lipid membranes under tension. The Journal of Chemical Physics 131:20.
Crossref
Crossref
G. Sharma, K. Rege, D.E. Budil, M. Yarmush & C. Mavroidis. (2009) Biological Force Measurement in a Protein-Based Nanoactuator. IEEE Transactions on Nanotechnology 8:6, pages 684-691.
Crossref
Crossref
Stefano V. Gullà, Gaurav Sharma, Peter Borbat, Jack H. Freed, Harishchandra Ghimire, Monica R. Benedikt, Natasha L. Holt, Gary A. Lorigan, Kaushal Rege, Constantinos Mavroidis & David E. Budil. (2009) Molecular-Scale Force Measurement in a Coiled-Coil Peptide Dimer by Electron Spin Resonance. Journal of the American Chemical Society 131:15, pages 5374-5375.
Crossref
Crossref
Carlos Alemán, Nikos Ch. Karayiannis, David Curcó, Katerina Foteinopoulou & Manuel Laso. (2009) Computer simulations of amorphous polymers: From quantum mechanical calculations to mesoscopic models. Journal of Molecular Structure: THEOCHEM 898:1-3, pages 62-72.
Crossref
Crossref
W. J. Briels. (2009) Transient forces in flowing soft matter. Soft Matter 5:22, pages 4401.
Crossref
Crossref
J. L. Suter, E. S. Boek & M. Sprik. (2008) Adsorption of a Sodium Ion on a Smectite Clay from Constrained Ab Initio Molecular Dynamics Simulations. The Journal of Physical Chemistry C 112:48, pages 18832-18839.
Crossref
Crossref
Carsten Hartmann. (2007) An Ergodic Sampling Scheme for Constrained Hamiltonian Systems with Applications to Molecular Dynamics. Journal of Statistical Physics 130:4, pages 687-711.
Crossref
Crossref
Carsten Hartmann & Christof Schütte. (2007) Comment on two distinct notions of free energy. Physica D: Nonlinear Phenomena 228:1, pages 59-63.
Crossref
Crossref
Daniel Trzesniak, Anna‐Pitschna E. Kunz & Wilfred F. van Gunsteren. (2006) A Comparison of Methods to Compute the Potential of Mean Force. ChemPhysChem 8:1, pages 162-169.
Crossref
Crossref
Eric Darve. 2007. Free Energy Calculations. Free Energy Calculations
119
170
.
Christophe Chipot, M. Scott Shell & Andrew Pohorille. 2007. Free Energy Calculations. Free Energy Calculations
1
31
.
Pablo Echenique & Iván Calvo. (2006) Explicit factorization of external coordinates in constrained statistical mechanics models. Journal of Computational Chemistry 27:14, pages 1748-1755.
Crossref
Crossref
Pablo Echenique, Iván Calvo & J. L. Alonso. (2006) Quantum mechanical calculation of the effects of stiff and rigid constraints in the conformational equilibrium of the alanine dipeptide. Journal of Computational Chemistry 27:14, pages 1733-1747.
Crossref
Crossref
Pablo Echenique & J. L. Alonso. (2006) Definition of Systematic, Approximately Separable, and Modular Internal Coordinates (SASMIC) for macromolecular simulation. Journal of Computational Chemistry 27:10, pages 1076-1087.
Crossref
Crossref
Ivaylo Ivanov, Bin Chen, Simone Raugei & Michael L. Klein. (2006)
Relative p
K
a
Values from First-Principles Molecular Dynamics: The Case of Histidine Deprotonation
. The Journal of Physical Chemistry B 110:12, pages 6365-6371.
Crossref
Crossref
Jiří Matoušek, Petr Kulhánek, Michal Čajan & Jaroslav Koča. (2005) Effect of Solvation on Pinched Cone−Pinched Cone Interconversion of Tetraethoxycalix[4]arene and Tetraethoxythiacalix[4]arene. The Journal of Physical Chemistry A 110:3, pages 861-867.
Crossref
Crossref
T. V. Tolpekina, W. K. den Otter & W. J. Briels. (2004) Nucleation free energy of pore formation in an amphiphilic bilayer studied by molecular dynamics simulations. The Journal of Chemical Physics 121:23, pages 12060-12066.
Crossref
Crossref
Sheng-Yong Yang, Paul Fleurat-Lessard, Iordan Hristov & Tom Ziegler. (2004)
Free Energy Profiles for the Identity S
N
2 Reactions Cl
-
+ CH
3
Cl and NH
3
+ H
3
BNH
3
: A Constraint
Ab Initio
Molecular Dynamics Study
. The Journal of Physical Chemistry A 108:43, pages 9461-9468.
Crossref
Crossref
Jérôme Hénin & Christophe Chipot. (2004) Overcoming free energy barriers using unconstrained molecular dynamics simulations. The Journal of Chemical Physics 121:7, pages 2904-2914.
Crossref
Crossref
C. Pastorino & Z. Gamba. (2003) Free-energy calculations of elemental sulphur crystals via molecular dynamics simulations. The Journal of Chemical Physics 119:4, pages 2147-2154.
Crossref
Crossref
W. K. den Otter & W. J. Briels. (2003) The bending rigidity of an amphiphilic bilayer from equilibrium and nonequilibrium molecular dynamics. The Journal of Chemical Physics 118:10, pages 4712-4720.
Crossref
Crossref
Jürgen Schlitter & Marco Klähn. (2003) A new concise expression for the free energy of a reaction coordinate. The Journal of Chemical Physics 118:5, pages 2057-2060.
Crossref
Crossref
Eric Darve & Andrew Pohorille. (2001) Calculating free energies using average force. The Journal of Chemical Physics 115:20, pages 9169-9183.
Crossref
Crossref
Surjit B. Dixit & Christophe Chipot. (2001) Can Absolute Free Energies of Association Be Estimated from Molecular Mechanical Simulations? The Biotin−Streptavidin System Revisited. The Journal of Physical Chemistry A 105:42, pages 9795-9799.
Crossref
Crossref