AMBER

From Academic Kids

AMBER (an acronym for Assisted Model Building and Energy Refinement) is a force field for molecular dynamics originally developed by Peter Kollman's group in the University of California, San Francisco. AMBER is also the name for the molecular dynamics simulation package associated with this force field, now coordinated by David A. Case at Scripps Research Institute. A notable use of AMBER is in the distributed computing project Folding@home where it was recently (as of October 15, 2004) in the simulation of protein folding.

The forcefield takes the form of <math> V_{(r^N)}=\sum_{bonds} \frac{1}{2} k_b (l-l_0)^2 + \sum_{angles} \frac{1}{2} k_a (\theta - \theta_0)^2 + \sum_{torsions} \frac{1}{2} V_n [1+cos(n \omega- \gamma)] +\sum_{j=1} ^{N-1} \sum_{i=j+1} ^N \left\{4\epsilon_{i,j}\left[\left(\frac{\sigma_{ij}}{r_{ij}} \right)^{12} - \left(\frac{\sigma_{ij}}{r_{ij}} \right)^6 \right]+ \frac{q_iq_j}{4\pi \epsilon_0 r_ij}\right\} <math>

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