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Recent "PMF" articles

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Monte Carlo free energy calculations using electronic structure methods
Daniel Matusek, Sebastien Osborne, and Alain St-Amant
The Journal of Chemical Physics 128 (15), 154110 (2008)
info:doi/10.1063/1.2890725
Posted by orbeckst and 1 other to thermodynamic integration HCN PMF force field MMBIF importance sampling on Tue Apr 22 2008 at 10:17 UTC | info | related
 
Calculation of free-energy differences and potentials of mean force by a multi-energy gap method
The Journal of Chemical Physics 128 (11), 114104 (2008)
info:doi/10.1063/1.2841942
Posted by orbeckst to PMF molecular dynamics Monte Carlo free energy on Tue Mar 25 2008 at 16:02 UTC | info | related
 
Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations
Anna C.V. Johansson and Erik Lindahl
Proteins: Structure, Function, and Bioinformatics 70 (4), 1332-44 (2008)
info:doi/10.1002/prot.21629
Posted by orbeckst to gromacs molecular dynamics helix PMF free energy on Sat Feb 09 2008 at 17:58 UTC | info | related
 
Calculation of PMF from the WHAM and FEP molecular dynamics simulations: Case study of the methane dimer in water
Chemical Physics Letters 452 (1-3), 72 (2008)
info:doi/10.1016/j.cplett.2007.12.017
Posted by orbeckst to molecular dynamics methane TIP3P water FEP free energy PMF on Fri Feb 01 2008 at 10:19 UTC | info | related
 
Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
Karunesh And and I Brooks
Proceedings of the National Academy of Sciences 104 (47), 18496-18501 (20 Nov 2007)
info:doi/10.1073/pnas.0706443104
Posted by orbeckst and 1 other to PMF molecular dynamics adenylate kinase free energy calculations on Sun Nov 25 2007 at 21:37 UTC | info | related
 
Potentials of Mean Force for Acetylcholine Unbinding from the Alpha7 Nicotinic Acetylcholine Receptor Ligand-Binding Domain
Journal of the American Chemical Society 128 (9), 3019 (2006)
info:doi/10.1021/ja057292u
Posted by orbeckst to binding free energy nAChR PMF on Mon Oct 22 2007 at 22:26 UTC | info | related
 
Electric-field-controlled water and ion permeation of a hydrophobic nanopore
The Journal of Chemical Physics 122 (23), 234706 (2005)
info:doi/10.1063/1.1927514
Posted by orbeckst and 1 other to Electric field molecular dynamics MD pores PMF water on Fri Oct 27 2006 at 03:08 UTC | info | related
 
A Hydrophobic Gate in an Ion Channel: The Closed State of the Nicotinic Acetylcholine Receptor
www.iop.org
Free energy calculations of a reduced model of the nicotinic receptor transmembrane domain show that the hydrophobic ring forms a desolvation barrier for the permeation of Na+ ions (but less so for Cl-).
Posted by orbeckst (who is an author) and 1 other with 1 comment to WHAM PMF hydrophobicity free energy calculations permeation nAChR on Wed Jul 26 2006 at 20:34 UTC | info | related
 
Role of Protein Flexibility in Ion Permeation: A Case Study in Gramicidin A -- Bastug et al. 90 (7): 2285 -- Biophysical Journal
www.biophysj.org
PMF of K+ in gA. Channel is maded increasingly more rigid.
Posted by orbeckst to ion channels flexibility Ions potential of mean force PMF gramicidin GA on Sun Jun 04 2006 at 04:00 UTC | info | related
 
Ion Permeation through a Narrow Channel: Using Gramicidin to Ascertain All-Atom Molecular Dynamics Potential of Mean Force Methodology and Biomolecular Force Fields
Toby W. Allen, Olaf S. Andersen, and Benoit Roux
Biophysical Journal 90 (10), 3447-68 (15 May 2006)
How to compute PMFs properly.
Posted by orbeckst to polarisability force field gromos amber charmm molecular dynamics free energy calculations PMF gramicidin on Fri Apr 21 2006 at 16:29 UTC | info | related

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