AMBERPLUS version 2010 is a patch that incorporates the following methods into one of the modules of AMBER, in particular sander, which carry outs energy minimization, molecular dynamics (MD), and NMR refinements. AMBERPLUS introduces: the TINKER tapering function for long-range electrostatic interactions the link atom method with a fixed value of the ratio of the Q1-QL bond length to the Q1-M1 bond length multi-configuration Shepard interpolation (MCSI) or electrostatically embedded multi-configuration Shepard interpolation (EE-MCSI) method as one of the methods for the quantum mechanical (QM) region of a combined QM/MM calculation; this is accomplished by using MCSI program The TINKER tapering function makes the electrostatic interactions become zero smoothly at a cutoff distance; it can be employed in order to conserve the total energy of the system with periodic boundary conditions without using Ewald summation. AMBERPLUS adds another type of link atom method for QM/MM calculations in sander, namely the multi- configuration Shepard interpolation (MCSI) method, which was previously called multi- configuration molecular mechanics (MCMM). The MCSI method enables one to generate semiglobal potential energy surfaces of reactive systems efficiently in the gas phase. The EE-MCSI method is an extension of the MCSI method; it can generate semiglobal potential energy surfaces in the presence of an electrostatic potential. In AMBERPLUS the combined EE-MCSI and molecular mechanical (EE-MCSI/MM) method is available, where the electrostatically embedded QM energy in a conventional combined quantum mechanical and molecular mechanical (QM/MM) method is replaced by the EE-MCSI potential energy. To install the AMBERPLUS version 2010, one requires AMBERTOOLS version 1.4 with bugfixes 1-16, AMBER version 11 with bugfixes 1-11, and MCSI version 2010.
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