Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective
نویسندگان
چکیده
منابع مشابه
Are current semiempirical methods better than force fields? A study from the thermodynamics perspective.
The semiempirical Hamiltonians MNDO, AM1, PM3, RM1, PDDG/MNDO, PDDG/PM3, and SCC-DFTB, when used as part of a hybrid QM/MM scheme for the simulation of biological molecules, were compared on their abilities to reproduce experimental ensemble averages at or near room temperatures for the model system alanine dipeptide in water. Free energy surfaces in the (phi, psi) dihedral angle space, (3)J(H(...
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Are current molecular dynamics force fields too helical?
Accurate force fields are essential for the success of molecular dynamics simulations. In apparent contrast to the conformational preferences of most force fields, recent NMR experiments suggest that short polyalanine peptides in water populate the polyproline II structure almost exclusively. To investigate this apparent contradiction, with its ramifications for the assessment of molecular forc...
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ژورنال
عنوان ژورنال: The Journal of Physical Chemistry A
سال: 2009
ISSN: 1089-5639,1520-5215
DOI: 10.1021/jp903474v