Author Instructions Checklist Adobe Acrobat Users -notes Tool Sheet Reprint Order Form Copyright Transfer Agreement Return Fax Form a Copy of Your Page Proofs for Your Article Journal of Computational Chemistry (jcc) Return To
نویسنده
چکیده
The assignment of atomic charges to a regular computational grid and the interpolation of forces from the grid back to the original atomic positions are crucial steps in a multigrid approach to the calculation of molecular forces. For purposes of grid assignment, atomic charges are modeled as truncated Gaussian distributions. The charge assignment and back interpolation methods are currently bottlenecks, and take up to one-third the execution time of the multigrid method each. Here, we propose alternative approaches to both charge assignment and back interpolation where convolution is used both to map Gaussian representations of atomic charges onto the grid and to map the forces computed at grid points back to atomic positions. These approaches achieve the same force accuracy with reduced run time. The proposed charge assignment and back interpolation methods scale better than baseline multigrid computations with both problem size and number of processors. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 000–000, 2005
منابع مشابه
Journal of Neuroscience Research the Site Contains One File, Containing: -author Instructions Checklist -adobe Acrobat Users -notes Tool Sheet -reprint Order Form -a Copy of Your Page Proofs for Your Article
Sons has made this article available to you online for faster, more efficient editing. Please follow the instructions below and you will be able to access a PDF version of your article as well as relevant accompanying paperwork. First, make sure you have a copy of Adobe Acrobat Reader software to read these files. Print out this file, and fill out the forms by hand. (If you do not wish to order...
متن کاملProteins: Structure, Function, and Genetics Author Instructions Checklist Adobe Acrobat Users -notes Tool Sheet Reprint Order Form Copyright Transfer Agreement Return Fax Form a Copy of Your Page Proofs for Your Article Proteins: Structure, Function, and Genetics
We investigated protein motions using normal modes within a database framework, determining on a large sample the degree to which normal modes anticipate the direction of the observed motion and were useful for motions classification. As a starting point for our analysis, we identified a large number of examples of protein flexibility from a comprehensive set of structural alignments of the pro...
متن کاملJournal of Medical Devices Journal Adobe Acrobat Users -notes Tool Sheet
A copy of your page proofs for your article Please read the page proofs carefully and: 1) indicate changes or corrections using e-annotation; 2) answer all queries; 3) proofread any tables and equations carefully; 4) check that any special characters have translated correctly. Your prompt attention to and return of page proofs will help expedite publication of your work. Thank you for your coop...
متن کاملProteins: Structure, Function, and Genetics Author Instructions Checklist Adobe Acrobat Users -notes Tool Sheet Reprint Order Form Return Fax Form a Copy of Your Page Proofs for Your Article Proteins: Structure, Function, and Genetics
We conducted a structural genomics analysis of the folds and structural superfamilies in the first 20 completely sequenced genomes by focusing on the patterns of fold usage and trying to identify structural characteristics of typical and atypical folds. We assigned folds to sequences using PSI-blast, run with a systematic protocol to reduce the amount of computational overhead. On average, fold...
متن کاملEndocrinology Reprint and Publication Charges 2010
RETURNING YOUR PROOF Please review the instructions below and indicate any necessary changes to your proofs. Keep a copy of the corrected proof for your records, and within 48 hours (two business days) return it to: [email protected]. We encourage you to return an annotated PDF by e-mail if possible. You may also fax it to 215-489-3196. If you choose to mail a hard copy, send it within two busin...
متن کامل