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	Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water [My Copy] Journal of Computational Chemistry, Vol. 31, No. 1. (2010), pp. 1-23. by Halvor S. Hansen, Philippe H. Hünenberger posted to pmf free-energy by agrossfield on 2009-11-24 14:03:15 as
	Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations [My Copy] Journal of Computational Chemistry, Vol. 31, No. 1. (2010), pp. 204-216. by Alexey K. Shaytan, Victor A. Ivanov, Konstantin V. Shaitan, Alexei R. Khokhlov posted to solvation pmf free-energy forcefield by agrossfield on 2009-11-24 13:57:39 as
	Binding free energy and counterion release for adsorption of the antimicrobial peptide lactoferricin B on a POPG membrane [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 3. (2009), 031911. by Igor S. Tolokh, Victor Vivcharuk, Bruno Tomberli, C. G. Gray posted to free-energy antimicrobial-peptide by agrossfield on 2009-10-23 17:16:16 as
	Generalized Langevin models of molecular dynamics simulations with applications to ion channels [My Copy] The Journal of Chemical Physics, Vol. 131, No. 13. (2009), 134102. by Dan Gordon, Vikram Krishnamurthy, Shin H. Chung posted to langevin ion-channel free-energy by agrossfield on 2009-10-07 20:57:15 as along with 1 person dlimmer
	Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages [My Copy] The Journal of Chemical Physics, Vol. 131, No. 13. (2009), 134110. by David D. L. Minh, John D. Chodera posted to free-energy by agrossfield on 2009-10-07 20:55:44 as along with 1 person dlimmer
	The calculation of chemical potential of organic solutes in dense liquid phases by using expanded ensemble Monte Carlo simulations [My Copy] The Journal of Chemical Physics, Vol. 131, No. 7. (2009), 074103. by Jaeeon Chang posted to free-energy enhanced-sampling by agrossfield on 2009-08-22 13:36:44 as along with 1 person dlimmer
	Accelerating flat-histogram methods for potential of mean force calculations [My Copy] The Journal of Chemical Physics, Vol. 131, No. 5. (2009), 054105. by Lorant Janosi, Manolis Doxastakis posted to free-energy pmf by agrossfield on 2009-08-07 20:39:51 as along with 1 person dlimmer
	Umbrella integration in two or more reaction coordinates [My Copy] The Journal of Chemical Physics, Vol. 131, No. 3. (2009), 034109. by Johannes Kästner posted to free-energy by agrossfield on 2009-07-21 20:50:02 as along with 1 person dlimmer
	Calculation of Free-Energy Differences by Confinement Simulations. Application to Peptide Conformers [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 29. (23 July 2009), pp. 9728-9740. by M. Cecchini, S. V. Krivov, M. Spichty, M. Karplus posted to free-energy network-model by agrossfield on 2009-07-17 21:49:00 as along with 1 person carlosjavierna
	Unorthodox uses of Bennett's acceptance ratio method [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Gerhard König, Stefan Bruckner, Stefan Boresch posted to free-energy by agrossfield on 2009-06-16 13:12:44 as along with 2 people ssomani RamuAnandakrishnan
	Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Dian Jiao, Jiajing Zhang, Robert E. Duke, Guohui Li, Michael J. Schnieders, Pengyu Ren posted to forcefield free-energy implicit-solvent ligand-binding by agrossfield on 2009-06-16 13:07:49 as along with 2 people and 1 group flbarroso sobolevnrm baker-group
	Lambda-dynamics free energy simulation methods. [My Copy] Journal of computational chemistry, Vol. 30, No. 11. (August 2009), pp. 1692-1700. by J. L. Knight, C. L. Brooks posted to free-energy lambda-dynamics by agrossfield on 2009-06-16 13:06:31 as along with 3 people and 1 group ibuch klexa sobolevnrm baker-group
	Absolute free energies estimated by combining precalculated molecular fragment libraries [My Copy] Journal of Computational Chemistry, Vol. 30, No. 11. (2009), pp. 1680-1691. by Xin Zhang, Artem B. Mamonov, Daniel M. Zuckerman posted to free-energy by agrossfield on 2009-06-16 13:05:57 as
	Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function [My Copy] Journal of Computational Chemistry, Vol. 30, No. 11. (2009), pp. 1622-1633. by Wonpil Im, Jinhyuk Lee, Taehoon Kim, Huan Rui posted to free-energy membrane-proteins by agrossfield on 2009-06-16 13:05:11 as
	The work-Hamiltonian connection and the usefulness of the Jarzynski equality for free energy calculations [My Copy] The Journal of Chemical Physics, Vol. 130, No. 17. (2009), 171102. by Eric N. Zimanyi, Robert J. Silbey posted to free-energy jarzynski by agrossfield on 2009-05-08 19:20:07 as along with 2 people dlimmer paulschlesinger
	Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations [My Copy] The Journal of Chemical Physics, Vol. 130, No. 16. (2009), 164906. by Marty F. Ytreberg posted to free-energy jarzynski ligand-binding by agrossfield on 2009-04-30 21:48:51 as
	Entropic Cost of Protein−Ligand Binding and Its Dependence on the Entropy in Solution [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Sheeba J. Irudayam, Richard H. Henchman posted to free-energy by agrossfield on 2009-04-28 02:32:03 as along with 2 people and 1 group mijam sobolevnrm baker-group
	Assessment of Nonequilibrium Free Energy Methods [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 16. (23 April 2009), pp. 5508-5519. by Benjamin P. Cossins, Sebastien Foucher, Colin M. Edge, Jonathan W. Essex posted to free-energy jarzynski by agrossfield on 2009-04-21 13:25:58 as
	Gaussian-Mixture Umbrella Sampling [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Paul Maragakis, Arjan van der Vaart, Martin Karplus posted to free-energy umbrella-sampling by agrossfield on 2009-04-03 13:55:21 as along with 2 people and 1 group willard sobolevnrm baker-group
	Computations of Standard Binding Free Energies with Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 8. (26 February 2009), pp. 2234-2246. by Yuqing Deng, Benoît Roux posted to free-energy ligand-binding by agrossfield on 2009-02-24 15:32:22 as along with 9 people and 2 groups anuragsethi flbarroso mikaellund sobolevnrm barry jmccammon willard carlosjavierna ibuch baker-group McCammon
	Free-Energy Profiles of Membrane Insertion of the M2 Transmembrane Peptide from Influenza A Virus [My Copy] Biophys. J., Vol. 95, No. 11. (1 December 2008), pp. 5021-5029. by In-Chul Yeh, Mark A. Olson, Michael S. Lee, Anders Wallqvist posted to free-energy implicit-membrane lipid-protein-interactions replica-exchange by agrossfield on 2008-11-19 14:24:19 as along with 1 person paulschlesinger
	Computing conformational free energy by deactivated morphing [My Copy] The Journal of Chemical Physics, Vol. 129, No. 13. (2008), 134102. by Sanghyun Park, Albert Y. Lau, Benoît Roux posted to free-energy by agrossfield on 2008-10-10 17:18:11 as along with 3 people and 1 group paddydu sobolevnrm sunhwan baker-group
	Dynamic Mechanism of Fatty Acid Transport across Cellular Membranes through FadL: Molecular Dynamics Simulations [My Copy] J. Phys. Chem. B, Vol. 112, No. 41. (16 October 2008), pp. 13070-13078. by Hanjun Zou, Mingyue Zheng, Xiaomin Luo, et al.Weiliang Zhu, Kaixian Chen, Jianhua Shen, Hualiang Jiang posted to free-energy membrane steered-md by agrossfield on 2008-10-10 16:50:37 as
	Free-energy landscape of mechanically unfolded model proteins: Extended Jarzinsky versus inherent structure reconstruction [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 78, No. 3. (2008) by Stefano Luccioli, Alberto Imparato, Alessandro Torcini posted to free-energy protein-folding wham by agrossfield on 2008-10-09 13:20:53 as
	A direct multiple histogram reweighting method for optimal computation of the density of states [My Copy] The Journal of Chemical Physics, Vol. 129, No. 12. (2008) by Michael K. Fenwick posted to free-energy wham by agrossfield on 2008-09-30 19:47:28 as
	Statistically optimal analysis of samples from multiple equilibrium states [My Copy] The Journal of Chemical Physics, Vol. 129, No. 12. (2008) by Michael R. Shirts, John D. Chodera posted to free-energy wham by agrossfield on 2008-09-30 19:35:00 as along with 1 person and 1 group mfajer McCammon
	On the Crooks fluctuation theorem and the Jarzynski equality [My Copy] The Journal of Chemical Physics, Vol. 129, No. 9. (2008) by L. Y. Chen posted to free-energy jarzynski by agrossfield on 2008-09-06 22:24:12 as along with 1 person yzlab
	Energy difference space random walk to achieve fast free energy calculations [My Copy] The Journal of Chemical Physics, Vol. 128, No. 19. (2008) by Donghong Min, Wei Yang posted to free-energy by agrossfield on 2008-05-29 14:17:10 as

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antimicrobial-peptide	82
coarse-grain	54
free-energy	28
membrane	24
ion-solvation	23
nmr	20
lipid-protein-interactions	20
membrane-proteins	19
gpcr	18
membrane-electrostatics	18
rhodopsin	17
implicit-membrane	16
pca	15
lipopeptide	11
rafts	11
replica-exchange	11
network-model	10
implicit-solvent	9
membrane-forcefield	8
protein-folding	8
pmf	6
forcefield	6
internal-water	6
jarzynski	6
ion-channel	6
electrostatics	5
b2ar	5
ligand-binding	5
pepducin	4
me	4
scattering	4
lipid-curvature	4
wham	4
waxs	4
solvation	3
phosphorus	3
membrane-fusion	3
langevin	3
defensin	3
membrane-theory	3
integrator	3
amyloid	3
thermostats	3
alamethicin	3
grand_canonical_ensemble	2
peptide	2
detergent	2
beta-adrenergic	2
isotropic-periodic-sum	2
magainin	2
cholesterol	2
protein-hydration	2
md	2
convergence	2
pores	2
protegrin	2
water	2
path-sampling	2
error-analysis	2
dpd	2
bacteriorhodopsin	2
glycophorin	2
multiscale	2
salt	2
enhanced-sampling	2
lattice	2
polarizability	2
flip-flop	1
allostery	1
modeling-software	1
lambda-dynamics	1
cecropin	1
unsaturated	1
helfrich	1
hydration	1
superposition	1
pore_size	1
pengyu	1
src	1
pore_formation	1
hiv_virus	1
charge	1
virus	1
dipole-lattice	1
porin	1
vesicles	1
field-theory	1
nmr_spectroscopy	1
micelles	1
demixing	1
hemagglutinin	1
finite-size-effect	1
loop-modeling	1
barrel-stave	1
polyunsaturated_fatty_acids	1
fission	1
ras	1
dendrite	1
colicin	1
nuclear_magnetic_resonance	1
lipid_bilayer	1
clustering	1
drug-development	1
fluoresence	1
error_distribution	1
flu	1
dye	1
dimers	1
ewald	1
umbrella-sampling	1
generalized-born	1
gay-berne	1
voltage_sensors	1
pressure-profile	1
neutron_diffraction	1
bicelles	1
hydrophobic-mismatch	1
polymer	1
lipid_membrane	1
prediction	1
structure	1
molecular_dynamics_simulations	1
fabp	1
walp	1
antibiotic-resistance	1
osmolytes	1
normal-modes	1
multiple-time-step	1
cryomicroscopy	1
inherent-structure	1
structure-prediction	1
shaw	1
hydrophobicity-scale	1
fluorination	1
nanotube	1
simulation	1
ions	1
rigid-body	1
hiv	1
methods	1
markov	1
g_protein_coupled_receptor	1
sevi	1
potassium_channel	1
crowding	1
steered-md	1

agrossfield's free-energy [28 articles] Export

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