Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide Export

@article{citeulike:4146315, abstract = {Approximate free energy surfaces and transition rates are presented for alanine dipeptide for a variety of force fields and implicit solvent models. Our calculations are based upon local minima, transition states and pathways characterised for each potential energy surface using geometry optimisation. The superposition approach employing only local minima and harmonic densities of states provides a representation of low-lying regions of the free energy surfaces. However, including contributions from the transition states of the potential energy surface and selected points obtained from displacements along the corresponding reaction vectors produces surfaces that compare quite well with results from replica exchange molecular dynamics. Characterising the local minima, transition states, normal modes, pathways, rate constants and free energy surfaces for each force field within this framework typically requires between one and five minutes cpu time on a single processor.}, author = {Strodel, Birgit and Wales, David J.}, citeulike-article-id = {4146315}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.cplett.2008.10.085}, citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0009261408014796}, day = {04}, doi = {10.1016/j.cplett.2008.10.085}, issn = {00092614}, journal = {Chemical Physics Letters}, keywords = {amino, articulo, coarse-grained, dialanine, free\_energy, hexapeptide, statistical\_mechanics}, month = {December}, number = {4-6}, pages = {105--115}, posted-at = {2009-03-07 12:18:52}, priority = {2}, title = {Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide}, url = {http://dx.doi.org/10.1016/j.cplett.2008.10.085}, volume = {466}, year = {2008} }

TY - JOUR ID - citeulike:4146315 L3 - citeulike-article-id:4146315 N2 - Approximate free energy surfaces and transition rates are presented for alanine dipeptide for a variety of force fields and implicit solvent models. Our calculations are based upon local minima, transition states and pathways characterised for each potential energy surface using geometry optimisation. The superposition approach employing only local minima and harmonic densities of states provides a representation of low-lying regions of the free energy surfaces. However, including contributions from the transition states of the potential energy surface and selected points obtained from displacements along the corresponding reaction vectors produces surfaces that compare quite well with results from replica exchange molecular dynamics. Characterising the local minima, transition states, normal modes, pathways, rate constants and free energy surfaces for each force field within this framework typically requires between one and five minutes cpu time on a single processor. IS - 4-6 JF - Chemical Physics Letters SN - 00092614 EP - 115 TI - Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide VL - 466 SP - 105 KW - amino KW - articulo KW - coarse-grained KW - dialanine KW - free_energy KW - hexapeptide KW - statistical_mechanics AU - Strodel, Birgit AU - Wales, David PY - 2008/12/04/ UR - http://dx.doi.org/10.1016/j.cplett.2008.10.085 ER -