Linked Life Data

16851719

Source:http://linkedlifedata.com/resource/pubmed/id/16851719

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
13
pubmed:dateCreated
2006-7-20
pubmed:abstractText
A comparison between two related methods, Schlitter's formula and quasiharmonic analysis, for calculating absolute entropies from the covariance matrix of atomic fluctuations using molecular dynamics (MD) simulations is presented. Calculations for a set of organic compounds in the gas phase are compared to the corresponding statistical thermodynamics results for translational and rotational entropies and to experimental data for vibrational entropies. Encouraging agreement is obtained for translational entropies, but for the rotational contribution, both methods fail to reproduce the theoretically calculated values. Absolute and relative vibrational entropies are found to be better reproduced using quasiharmonic analysis compared to Schlitter's formula. For rotational entropies, we propose a method based on the variances in Euler angles, which gives good agreement with theory. Alternative methods for estimating translational entropies based on principal root mean-square (rms) fluctuations of the center of mass are also presented, and these reproduce theoretically calculated values well. These methodologies are applied to the binding of benzene to T4-lysozyme, where close agreement with the literature is obtained for translational and rotational entropies.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Apr
pubmed:issn
1520-6106
pubmed:author
pubmed:issnType
Print
pubmed:day
7
pubmed:volume
109
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
6448-56
pubmed:meshHeading
pubmed:year
2005
pubmed:articleTitle
Absolute and relative entropies from computer simulation with applications to ligand binding.
pubmed:affiliation
Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden.
pubmed:publicationType
Journal Article, Comparative Study, Research Support, Non-U.S. Gov't