Abstract
A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA)9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.
Highlights
Molecular dynamic (MD) simulation plays an increasingly important role in the study of structural and dynamical properties of biomolecules at the atomic level (Karplus and Petsko, 1990; Cheatham and Kollman, 2000; Karplus and McCammon, 2002)
To further improve the accuracy and efficiency of the ab initio molecular dynamic (AIMD) simulations for protein, in this work, we presented a force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method and checked its performance in the AIMD simulations for several systems
Fragment-based energies of individual residues and interaction energies of residues that form backbone hydrogen bonds are calculated by quantum mechanics
Summary
Molecular dynamic (MD) simulation plays an increasingly important role in the study of structural and dynamical properties of biomolecules at the atomic level (Karplus and Petsko, 1990; Cheatham and Kollman, 2000; Karplus and McCammon, 2002). In our previous study (Liu et al, 2015), a fragment based approach is presented for AIMD simulation of protein In this approach, the potential energy and atomic forces of the studied protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EEGMFCC) method (Wang et al, 2013). The potential energy and atomic forces of the studied protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EEGMFCC) method (Wang et al, 2013) This AIMD approach had been applied to MD simulation of a small benchmark protein Trpcage in both gas phase and in solution. This approach will balance the forces of the fragments and conserve the total energy of the system
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