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. 2014 May 1;10(7):2677–2689. doi: 10.1021/ct500090q

Table 1. Biomolecular Model Systems Simulated with Accelerated Molecular Dynamics (aMD) in the Present Studya.

system Nres Natoms cMD aMD dihedral/dual-boost ΔVavg (kcal/mol) σΔV (kcal/mol) δΔV (kcal/mol)
alanine dipeptide 2 1912 1000 ns 20 ns × 5 dihedral-boost 3.1 1.8 11.7
        20 ns  × 5, 1000 ns dual-boost 4.2 2.1 18.5
chignolin 10 6773 1000 ns × 2 300 ns  × 3 dual-boost 8.5 3.2 31.9
Trp-cage 20 34 370 1000 ns  × 2 500 ns  × 4 dual-boost 38.8 7.0 70.8
a

Nres and Natoms are the number of residues and system atoms, respectively. ΔVavg, σΔV, and δΔV are the average, standard deviation, and range (maximum–minimum) of the aMD boost potential, ΔV.