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Items: 1 to 20 of 90

1.

Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase.

Pham TT, Shirts MR.

J Chem Phys. 2012 Mar 28;136(12):124120. doi: 10.1063/1.3697833.

PMID:
22462848
2.

Identifying low variance pathways for free energy calculations of molecular transformations in solution phase.

Pham TT, Shirts MR.

J Chem Phys. 2011 Jul 21;135(3):034114. doi: 10.1063/1.3607597.

PMID:
21786994
3.

Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 1. Removal of Uncharged Atomic Sites.

Naden LN, Pham TT, Shirts MR.

J Chem Theory Comput. 2014 Mar 11;10(3):1128-49. doi: 10.1021/ct4009188.

PMID:
26580188
6.

Linear-scaling soft-core scheme for alchemical free energy calculations.

Buelens FP, Grubm├╝ller H.

J Comput Chem. 2012 Jan 5;33(1):25-33. doi: 10.1002/jcc.21938. Epub 2011 Sep 26.

PMID:
21953650
7.

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations.

Gapsys V, Seeliger D, de Groot BL.

J Chem Theory Comput. 2012 Jul 10;8(7):2373-82. doi: 10.1021/ct300220p. Epub 2012 Jun 6.

PMID:
26588970
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10.

Efficient and precise solvation free energies via alchemical adiabatic molecular dynamics.

Abrams JB, Rosso L, Tuckerman ME.

J Chem Phys. 2006 Aug 21;125(7):074115.

PMID:
16942330
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14.

The parameterization and validation of generalized born models using the pairwise descreening approximation.

Michel J, Taylor RD, Essex JW.

J Comput Chem. 2004 Nov 15;25(14):1760-70.

PMID:
15362133
15.

Tracing the minimum-energy path on the free-energy surface.

Fleurat-Lessard P, Ziegler T.

J Chem Phys. 2005 Aug 22;123(8):084101.

PMID:
16164276
16.

Accurate free energy calculation along optimized paths.

Chen C, Xiao Y.

J Comput Chem. 2010 May;31(7):1368-75. doi: 10.1002/jcc.21420.

PMID:
19859916
18.
19.

Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration.

Bruckner S, Boresch S.

J Comput Chem. 2011 May;32(7):1320-33. doi: 10.1002/jcc.21712. Epub 2010 Dec 31.

PMID:
21425289
20.

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