✦ LIBER ✦

Efficient parallelization of the energy, surface, and derivative calculations for internal coordinate mechanics

✍ Scribed by Maxim Totrov; Ruben Abagyan

Publisher: John Wiley and Sons
Year: 1994
Tongue: English
Weight: 949 KB
Volume: 15
Category: Article
ISSN: 0192-8651
DOI: 10.1002/jcc.540151006

No coin nor oath required. For personal study only.

✦ Synopsis

An efficient algorithm for parallelization of a molecular mechanics program operating in the space of internal coordinates such as dihedral angles, bond angles, and bond lengths is described. The iterative procedure to calculate analytical energy derivatives with respect to the internal coordinates was modified to allow parallelization. Computationally intensive modules that calculate energy and its derivatives, solvent-accessible surface, electrostatic polarization energy and that update lists of interactions were parallelized with nearly 100% efficiency. The proposed strategy for the shared-memory computer architecture is easily scalable and requires minimum changes in a program code. The overall speedup for a realistic calculation minimizing the energy of a myoglobin reaches a factor of 3 for 4 processors. 0 1994 by John Wiley & Sons, Inc .

📜 SIMILAR VOLUMES

Parallel algorithm for efficient calcula

Parallel algorithm for efficient calculation of second derivatives of conformational energy function in internal coordinates

✍ Nakamura, Shugo; Ikeguchi, Mitsunori; Shimizu, Kentaro 📂 Article 📅 1998 🏛 John Wiley and Sons 🌐 English ⚖ 219 KB 👁 1 views

A parallel algorithm for efficient calculation of the second Ž . derivatives Hessian of the conformational energy in internal coordinates is proposed. This parallel algorithm is based on the masterrslave model. A master processor distributes the calculations of components of the Hessian to one or mo

Efficient computation of potential energ

Efficient computation of potential energy first and second derivatives for molecular dynamics, normal coordinate analysis, and molecular mechanics calculations

✍ Robert E. Tuzun; Donald W. Noid; Bobby G. Sumpter 📂 Article 📅 1996 🏛 John Wiley and Sons 🌐 English ⚖ 711 KB

## Abstract By using two‐ and three‐body internal coordinates and their derivatives as intermediates, it is possible to enormously simplify formulas for three‐ and four‐body internal coordinates and their derivatives. Using this approach, simple formulas are presented for stretch (two‐body), two ty

An efficient parallel algorithm for the

An efficient parallel algorithm for the calculation of canonical MP2 energies

✍ Jon Baker; Peter Pulay 📂 Article 📅 2002 🏛 John Wiley and Sons 🌐 English ⚖ 111 KB

## Abstract We present the parallel version of a previous serial algorithm for the efficient calculation of canonical MP2 energies (Pulay, P.; Saebo, S.; Wolinski, K. Chem Phys Lett 2001, 344, 543). It is based on the Saebo–Almlöf direct‐integral transformation, coupled with an efficient prescreeni

A general machine algorithm for the calc

A general machine algorithm for the calculation of derivatives of moments of inertia with respect to internal coordinates

✍ E.Jean Jacob; H.Bradford Thompson 📂 Article 📅 1972 🏛 Elsevier Science 🌐 English ⚖ 265 KB

A more accurate potential energy surface

A more accurate potential energy surface and quantum mechanical cross section calculations for the F+ H2 reaction

✍ Steven L. Mielke; Gillian C. Lynch; Donald G. Truhlar; David W. Schwenke 📂 Article 📅 1993 🏛 Elsevier Science 🌐 English ⚖ 592 KB

A new potential energy surface (called 6SEC) obtained by iterative refinement of the previously published SSEC surface is presented. The new surface was obtained using accurate threedimensional quantum mechanical scattering calculations to test the effects of various modifications of the SSEC surfac

New out-of-plane angle and bond angle in

New out-of-plane angle and bond angle internal coordinates and related potential energy functions for molecular mechanics and dynamics simulations

✍ Lee, Sang-Ho; Palmo, Kim; Krimm, Samuel 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 315 KB 👁 2 views

With currently used definitions of out-of-plane angle and bond angle internal coordinates, Cartesian derivatives have singularities, at "r2 in the former case and in the latter. If either of these occur during molecular mechanics or dynamics simulations, the forces are not well defined. To avoid suc