17 research outputs found
The Effective Fragment Potential: Small Clusters and Radial Distribution Functions
The effective fragment potential (EFP) method for treating solventeffects provides relative energies and structures that are in excellent agreement with the analogous fully quantum [i.e., Hartree-Fock (HF), density functional theory(DFT), and second order perturbation theory (MP2)] results for small water clusters. The ability of the method to predict bulk water properties with a comparable accuracy is assessed by performing EFP molecular dynamics simulations. The resulting radial distribution functions (RDF) suggest that as the underlying quantum method is improved from HF to DFT to MP2, the agreement with the experimental RDF also improves. The MP2-based EFP method yields a RDF that is in excellent agreement with experiment
The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds
We extend the effective fragment molecular orbital method (EFMO) into
treating fragments connected by covalent bonds. The accuracy of EFMO is
compared to FMO and conventional ab initio electronic structure methods for
polypeptides including proteins. Errors in energy for RHF and MP2 are within 2
kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides
similar to FMO but obtained two to five times faster. For proteins, the errors
are also within a few kcal/mol of the FMO results. We developed both the RHF
and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures
had an RMSD of 0.40 and 0.44 {\AA} for RHF and MP2, respectively.Comment: Revised manuscrip