Molecular dynamics programs

Procacci P, Darden T A, Paci E and Marchi M 1997 ORAC a molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions J. Comput. Chem. 18 1848-62... 

Nelson, M., Humphrey, W., Gursoy, A., Dalke, A., Kale, L., Skeel, R.D., Schul-ten, K. NAMD - A parallel, object-oriented molecular dynamics program. Int. J. Supercomputing Applications and High Performance Computing 10 (1996) 251-268. 

K. Schulten. NAMD—a parallel, object-oriented molecular dynamics program. Inti. J. Supercomput. Applies. High Performance Computing, 10 251-268, 1996. 

Y. Hwang, R. Das, F. H. Saltz, M. Hadoscek and B. R. Brooks, Parallelizing molecular dynamics programs for distributed-memory machines , IEEE Computational Science and Engineering, Vol 2, no 2, 18-29, 1995. 

In the second step, the spatial restraints and the CHARMM22 force field tenns enforcing proper stereochemistry [80,81] are combined into an objective function. The general form of the objective function is similar to that in molecular dynamics programs such as CHARMM22 [80]. The objective function depends on the Cartesian coordinates of —10,000 atoms (3D points) that form a system (one or more molecules) ... 

There are many molecular dynamics programs available for simulations, and the book by Allen and Tildesley [6] provides a very helpful introduction for anyone who wishes to perform simulations. The key points are ... 

Fig. 9.5 Molecular dimensions of the PLA-backbone using the molecular dynamics program (MM2 in Quantum CAChe) with van der Waals radii taken into consideration. Optimization of structure is based on minimization of the total energy of the molecular system.

J. Marelius, K. Kolmodin, 1. Feierberg, and J. Aqvist, Q A molecular dynamics program... 

The statistical perturbation theory arising from the classical work of Zwanzig34 and its detailed implementation in a molecular dynamics program for computation of free energies is described in detail elsewhere.35 36 We give a very brief description of the method for the sake of completeness. The total Hamiltonian of a system may be written as the sum of the Hamiltonian (Ho) of the unperturbed system and the perturbation (Hi) ... 

Several groups have implemented their own ab initio molecular dynamics programs. Tab. 1.2 lists some of the most frequently used software ... 

The study of the enantioselective hydrosilylation reaction was performed with a series of combined quantum mechanics/molecular mechanics (QM/MM) calculations [26, 30] within the computational scheme of ab initio (AIMD) (Car-Parrinello) [62] molecular dynamics. The AIMD approach has been described in a number of excellent reviews [63-66], AIMD as well as hybrid QM/MM-AIMD calculations [26, 47] were performed with the ab initio molecular dynamics program CPMD [67] based on a pseudopotential framework, a plane wave basis set, and periodic boundary conditions. We have recently developed an interface to the CPMD package in which the coupling with a molecular mechanics force field has been implemented [26, 68],... 

The early version of the molecular dynamics program CHARMM (22) also... 

As instructors of physical chemistry, we all too often hear comments like the one in the title of this chapter. The prevailing attitude with which many students approach physical chemistry is one of fear for their academic survival. The concerns they have are not so much with the chemistry but with the math. For some students, the physical chemistry course is the first time they must authentically apply advanced mathematical concepts to solve real problems. Instructors can facilitate this transformation with exercises that demand critical thinking skills, but developing such materials requires extensive time and talent. The Virtual Substance molecular dynamics program is a powerful tool in our efforts as educators to help students successfully transition from abstract knowledge of mathematics to its application to scientific concepts. 

Marelius J, Kolmodin K, Feierberg I, Aqvist J (1998) Q a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems. J Mol Graph Model 16(4-6) 213-225, 261... 

The electronic structures and chemical bonding of lithium vanadium oxide were calculated by the DV-Xa method [10,11] using the program code [12]. The population analysis was made according to Mulliken [13]. The ab initio total-energy and molecular dynamics program VASP [14-16], based on the density... 

The experiments at the Pohang Accelerator Laboratory were supported in part by MOST and Pohang Iron and Steel (POSCO). Special thank to Isao Tanaka for supporting the ab initio total-energy and molecular dynamics program VASP (Vienna ab initio simulation package). 

Hutter J et at. (2007) Car-Parrinello Molecular Dynamics An Ab Initio Electronic Structure and Molecular Dynamics Program, see www.cpmd.org. 

T. P. Straatsma and J. A. McCammon, J. Comput. Chem., 11, 943 (1990). ARGOS, a Vectorized General Molecular Dynamics Program. 

This volume has two appendices. The first is a compilation by Professors Fiji Osawa and Kenny B. Lipkowitz of published molecular mechanics parameters. All too frequently, it seems, a program employing an empirical force field chokes on a structure for which it has no parameters. The tabulation in Appendix 1 will help users of molecular mechanics and molecular dynamics programs track down supplemental parameters required for their calculations. 

Our ultimate goal is the simulation of alloys and their behavior under conditions of elevated temperature. Accordingly, empirical multibody potentials present an attractive combination of physical accuracy and computational efficiency. To facilitate simulation under the widest possible variety of conditions of temperature, pressure, and surface tension, we decided to incorporate a multibody potential function for copper into a widely used, commercially available molecular dynamics program. We chose CHARMM [35], because of its widespread use, constant pressure/ temperature/surface tension capabilities, and reliability. 

The CHARMM code, version c25bl, was chosen for integration with the metal potential. CHARMM is a multi-purpose molecular dynamics program [35], which uses empirical potential energy functions to simulate a variety of systems, including proteins, nucleic acids, lipids, sugars and water. The availability of periodic boundary conditions of various lattice types (for example cubic and orthorhombic) makes it possible to treat solids as well as liquids. 

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