## Abstract Molecular dynamics simulations of Ca^+2^ ions near protein were performed with three force fields: GROMOS96, OPLSβAA, and CHARMM22. The simulations reveal major, forceβfield dependent, inconsistencies in the interaction between the Ca^+2^ ions with the protein. The variations are attrib
Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins
β Scribed by Stewart A. Adcock; J. Andrew McCammon
- Publisher
- John Wiley and Sons
- Year
- 2006
- Weight
- 8 KB
- Volume
- 37
- Category
- Article
- ISSN
- 0931-7597
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## Abstract The structure of the general classical trajectory FORTRAN code is discussed for use in molecular dynamics simulations of polymer processes. Substantial reductions in the number of mathematical operations in the code are achieved by using statement functions, modifying the ususal chain r
We have performed 128 folding and 45 unfolding molecular dynamics runs of chymotrypsin inhibitor 2 (CI2) with an implicit solvation model for a total simulation time of 0.4 microseconds. Folding requires that the three-dimensional structure of the native state is known. It was simulated at 300 K by
Steered molecular dynamics (SMD), a computer simulation method for studying force-induced reactions in biopolymers, has been applied to investigate the response of protein domains to stretching apart of their terminal ends. The simulations mimic atomic force microscopy and optical tweezer experiment