✦ LIBER ✦

vmdICE: A plug-in for rapid evaluation of molecular dynamics simulations using VMD

✍ Scribed by Bernhard Knapp; Nadja Lederer; Ulrich Omasits; Wolfgang Schreiner

Publisher: John Wiley and Sons
Year: 2010
Tongue: English
Weight: 435 KB
Volume: 31
Category: Article
ISSN: 0192-8651
DOI: 10.1002/jcc.21581

No coin nor oath required. For personal study only.

📜 SIMILAR VOLUMES

FAMUSAMM: An algorithm for rapid evaluat

FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations

✍ Eichinger, M.; Grubm�ller, H.; Heller, H.; Tavan, P. 📂 Article 📅 1997 🏛 John Wiley and Sons 🌐 English ⚖ 430 KB 👁 2 views

Within molecular dynamics simulations of protein᎐solvent systems the exact evaluation of long-range Coulomb interactions is computationally demanding and becomes prohibitive for large systems. Conventional truncation methods circumvent that computational problem, but are hampered by serious artifact

A model for the dynemicin-A cleavage of

A model for the dynemicin-A cleavage of DNA using molecular dynamics simulation

✍ Mario G. Cardozo; A. J. Hopfinger 📂 Article 📅 1993 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 903 KB

Does Amination of Formaldehyde Proceed T

Does Amination of Formaldehyde Proceed Through a Zwitterionic Intermediate in Water? Fragment Molecular Orbital Molecular Dynamics Simulations by Using Constraint Dynamics

✍ Makoto Sato; Hiroshi Yamataka; Yuto Komeiji; Yuji Mochizuki; Tatsuya Nakano 📂 Article 📅 2010 🏛 John Wiley and Sons 🌐 English ⚖ 322 KB 👁 1 views

A new set of molecular mechanics paramet

A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides

✍ Sanghyun Park; Randall J. Radmer; Teri E. Klein; Vijay S. Pande 📂 Article 📅 2005 🏛 John Wiley and Sons 🌐 English ⚖ 163 KB

## Abstract Recently, the importance of proline ring pucker conformations in collagen has been suggested in the context of hydroxylation of prolines. The previous molecular mechanics parameters for hydroxyproline, however, do not reproduce the correct pucker preference. We have developed a new set

Qmd-plot: A graphical utility for rapid

Qmd-plot: A graphical utility for rapid preliminary analysis of time series of fluctuating data, developed in the context of molecular dynamics simulations

✍ Sam Kalat; Geoff Mann; Jan Hermans 📂 Article 📅 2001 🏛 John Wiley and Sons 🌐 English ⚖ 219 KB

## Abstract Qmd‐plot is a utility to obtain rapid information about past or on‐going simulations, or real‐time data collections, in the form of graphs of recorded variables (__x__,__y__,…), as __x__–__y__ plots or as a function of simulated or real time. Time series records in the data file must be

Restrained molecular dynamics simulation

Restrained molecular dynamics simulations of HIV-1 protease: The first step in validating a new target for drug design

✍ Alexander L. Perryman; Jung-Hsin Lin; J. Andrew McCammon 📂 Article 📅 2006 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 804 KB

## Abstract To test the anticorrelated relationship that was recently displayed in conventional molecular dynamics (MD) simulations, several different restrained MD simulations on a wild type and on the V82F/I84V drug‐resistant mutant of HIV‐1 protease were performed. This anticorrelated relationsh