Ion permeation simulations by Gromacs-an example of high performance molecular dynamics

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 (C) 2010 John Wiley & Sons, Ltd.