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Items: 1 to 20 of 105

1.

Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units.

Lindert S, Bucher D, Eastman P, Pande V, McCammon JA.

J Chem Theory Comput. 2013 Nov 12;9(11):4684-4691.

2.

Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.

Peng X, Zhang Y, Chu H, Li G.

J Comput Chem. 2016 Mar 5;37(6):614-22. doi: 10.1002/jcc.24227.

PMID:
26493154
3.

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics.

Pierce LC, Salomon-Ferrer R, Augusto F de Oliveira C, McCammon JA, Walker RC.

J Chem Theory Comput. 2012 Sep 11;8(9):2997-3002.

4.

Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field.

Bradshaw RT, Essex JW.

J Chem Theory Comput. 2016 Aug 9;12(8):3871-83. doi: 10.1021/acs.jctc.6b00276.

5.

Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field.

Mohamed NA, Bradshaw RT, Essex JW.

J Comput Chem. 2016 Dec 15;37(32):2749-2758. doi: 10.1002/jcc.24500.

6.

Polarizable molecular dynamics in a polarizable continuum solvent.

Lipparini F, Lagardère L, Raynaud C, Stamm B, Cancès E, Mennucci B, Schnieders M, Ren P, Maday Y, Piquemal JP.

J Chem Theory Comput. 2015 Feb 10;11(2):623-34. doi: 10.1021/ct500998q.

7.

Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.

Nessler IJ, Litman JM, Schnieders MJ.

Phys Chem Chem Phys. 2016 Nov 9;18(44):30313-30322.

PMID:
27524378
8.

Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure.

Piquemal JP, Perera L, Cisneros GA, Ren P, Pedersen LG, Darden TA.

J Chem Phys. 2006 Aug 7;125(5):054511.

PMID:
16942230
9.

Current status of the AMOEBA polarizable force field.

Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA Jr, Head-Gordon M, Clark GN, Johnson ME, Head-Gordon T.

J Phys Chem B. 2010 Mar 4;114(8):2549-64. doi: 10.1021/jp910674d.

10.

Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: II. Toward massively parallel computations using smooth particle mesh Ewald.

Lagardère L, Lipparini F, Polack É, Stamm B, Cancès É, Schnieders M, Ren P, Maday Y, Piquemal JP.

J Chem Theory Comput. 2015 Jun 9;11(6):2589-99. doi: 10.1021/acs.jctc.5b00171.

PMID:
26575557
11.

Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field.

Manzoni F, Söderhjelm P.

J Comput Aided Mol Des. 2014 Mar;28(3):235-44. doi: 10.1007/s10822-014-9733-3.

PMID:
24577872
12.

Accurate Evaluation of Ion Conductivity of the Gramicidin A Channel Using a Polarizable Force Field without Any Corrections.

Peng X, Zhang Y, Chu H, Li Y, Zhang D, Cao L, Li G.

J Chem Theory Comput. 2016 Jun 14;12(6):2973-82. doi: 10.1021/acs.jctc.6b00128.

PMID:
27171823
13.

Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald.

Lagardère L, Lipparini F, Polack É, Stamm B, Cancès É, Schnieders M, Ren P, Maday Y, Piquemal JP.

J Chem Theory Comput. 2014 Feb 28;10(4):1638-1651.

14.
15.

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design.

Vanommeslaeghe K, MacKerell AD Jr.

Biochim Biophys Acta. 2015 May;1850(5):861-71. doi: 10.1016/j.bbagen.2014.08.004. Review.

16.

Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics.

Doshi U, Hamelberg D.

Biochim Biophys Acta. 2015 May;1850(5):878-88. doi: 10.1016/j.bbagen.2014.08.003. Review.

PMID:
25153688
17.

Ab Initio Extension of the AMOEBA Polarizable Force Field to Fe(2.).

Semrouni D, Isley WC 3rd, Clavaguéra C, Dognon JP, Cramer CJ, Gagliardi L.

J Chem Theory Comput. 2013 Jul 9;9(7):3062-71. doi: 10.1021/ct400237r.

PMID:
26583987
18.
19.

Development of AMOEBA force field for 1,3-dimethylimidazolium based ionic liquids.

Starovoytov ON, Torabifard H, Cisneros GA.

J Phys Chem B. 2014 Jun 26;118(25):7156-66. doi: 10.1021/jp503347f.

PMID:
24901255
20.

Current status of protein force fields for molecular dynamics simulations.

Lopes PE, Guvench O, MacKerell AD Jr.

Methods Mol Biol. 2015;1215:47-71. doi: 10.1007/978-1-4939-1465-4_3.

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