Paper Citing NAMD - Abstract
Nemkevich, Alexandra; Buergi, Hans-Beat; Spackman, Mark A.; Corry, Ben
Molecular dynamics simulations of structure and dynamics of organic molecular crystals
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:14916-14929, 2010
A set of model compounds covering a range of polarity and flexibility have been simulated using GAFF, CHARMM22, OPLS and MM3 force fields to examine how well classical molecular dynamics simulations can reproduce structural and dynamic aspects of organic molecular crystals. Molecular structure, crystal structure and thermal motion, including molecular reorientations and internal rotations, found from the simulations have been compared between force fields and with experimental data. The MM3 force field does not perform well in condensed phase simulations, while GAFF, CHARMM and OPLS perform very similarly. Generally molecular and crystal structure are reproduced well, with a few exceptions. The atomic displacement parameters (ADPs) are mostly underestimated in the simulations with a relative error of up to 70%. Examples of molecular reorientation and internal rotation, observed in the simulations, include in-plane reorientations of benzene, methyl rotations in alanine, decane, isopropylcyclohexane, pyramidal inversion of nitrogen in amino group and rotation of the whole group around the C-N bond. Frequencies of such dynamic processes were calculated, as well as thermodynamic properties for reorientations in benzene and alanine. We conclude that MD simulations can be used for qualitative analysis, while quantitative results should be taken with caution. It is important to compare the outcomes from simulations with as many experimental quantities as available before using them to study or quantify crystal properties not available from experiment.
