Paper Citing NAMD - Abstract
Bastug, T.; Kuyucak, S.
Molecular dynamics simulations of calcium binding in gramicidin A
CHEMICAL PHYSICS LETTERS, 424:82-85, JUN 12 2006
An important issue in molecular dynamics. (MD) simulations of biomolecules is whether membrane proteins can be described using nonpolarizable force fields. To shed further light into this question, we study calcium ion binding and blocking of the gramicidin A channel which has not been investigated in MD simulations before. Potential of mean force calculations for calcium and potassium ions using a nonpolarizable force field reveal that calcium binding to the channel is much weaker compared to potassium, and hence calcium block of potassium current cannot be described. Inclusion of polarization interaction in force fields may help to rectify this problem. (c) 2006 Elsevier B.V. All rights reserved.
