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Fast and accurate molecular dynamics simulation of a protein using a special-purpose computer

✍ Scribed by Komeiji, Yuto; Uebayasi, Masami; Takata, Ryo; Shimizu, Akihiro; Itsukashi, Keiji; Taiji, Makoto

Publisher: John Wiley and Sons
Year: 1997
Tongue: English
Weight: 428 KB
Volume: 18
Category: Article
ISSN: 0192-8651
DOI: 10.1002/(sici)1096-987x(199709)18:12<1546::aid-jcc11>3.0.co;2-i

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✦ Synopsis

a The 10-ps configuration of each trajectory was used as the initial configuration. The system was simulated for 5 ps using a ( ) microcanonical ensemble with various time steps. Then, the RMSF E and the computation time was examined. r tot b ( ) Hard forces H : bond, angle, and torsion. c ( ) Medium force M : vdW. d ( ) Soft force S : electrostatic. e ( ) Computation time s consumed per 1 fs MD.

f This condtion was adopted for further MD simulations.

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