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Ion permeation simulations by Gromacs—an example of high performance molecular dynamics
Author(s) -
Krüger J.,
Fels G.
Publication year - 2010
Publication title -
concurrency and computation: practice and experience
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.309
H-Index - 67
eISSN - 1532-0634
pISSN - 1532-0626
DOI - 10.1002/cpe.1666
Subject(s) - permeation , ion channel , ion , molecular dynamics , computer science , membrane , dementia , acetylcholine receptor , chemistry , neuroscience , materials science , receptor , computational chemistry , psychology , disease , medicine , biochemistry , organic chemistry , pathology
The loss of inter‐neuron communication is related to many neuronal diseases such as Alzheimer's dementia. The nicotinic acetylcholine receptor (nAChR) plays a crucial role in this process and is severely affected upon disease progression. Successful therapy approaches rely on modulation of response signals, initiated by the flux of ions through the receptor integrated ion channel at the post‐synaptic membrane. We present here the comparison of two methods for calculating the energy barrier of nAChR mediated ion permeation, in terms of accuracy and performance. Detailed descriptions of archetypical Gromacs characteristics are given offering better insight into computational service providers to meet the needs of scientists. Copyright © 2010 John Wiley & Sons, Ltd.