Amber

: For America's Missing: Broadcast Emergency Response, see AMBER Alert.

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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.

Related Topics:
Acronym - Force field - Molecular dynamics - Peter Kollman - University of California, San Francisco - Package - Scripps Research Institute - Distributed computing - Folding@home - October 15 - 2004 - Protein folding

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The force field takes the form of

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V(r^N)=sum_{bonds} rac{1}{2} k_b (l-l_0)^2 + sum_{angles} rac{1}{2} k_a ( heta - heta_0)^2

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+ sum_{torsions} rac{1}{2} V_n

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+sum_{j=1} ^{N-1} sum_{i=j+1} ^N left{4epsilon_{i,j}left+ rac{q_iq_j}{4pi epsilon_0 r_{ij}^2} ight}

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Some explanation for the terms in the force field expression:

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• First term (summing over bonds): in molecular geometry some forces are computed from chemical bonds between atomic pairs.
• Second term (summing over angles): Forces between atoms in the same molecule may arise even though the atoms are not themselves bonded side-by-side. The calculation of such forces involve the angles of the bonds that join the atoms.
• Third term (summing over torsions): Atoms and groups of atoms may exert forces on each other.
• Fourth term (electrostatic forces): The value $r\_\{ij\}$ is a vector. Also note that the argument $r\_N$ on the left-hand side is a vector, which gives the position of each point in the volume containing the molecules. The vector $r\_\{ij\}$ is a displacement vector between two vectors $r\_i$ and $r\_j$. Some forces caused by charges arising from ionization and dipoles are fairly weak (due to cancellation by other charges) and are thus reduced by a power of 6 or even 12 on the displacement vector $r\_\{ij\}$. Charges that are not cancelled cause a force proportional to $r\_\{ij\}^2$.

Strangely, the electrostatic term appears to be constant as it is computed over all points, which are independent of the point r_N specified by the argument on the left-hand side. Perhaps the electrostatic term needs to be combined with r_N by a dot product.

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