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. Author manuscript; available in PMC: 2009 Apr 17.
Published in final edited form as: J Comput Chem. 2009 Apr 15;30(5):673–699. doi: 10.1002/jcc.21005

Table III.

Overview of the details of the move sets employed for individual systems discussed in the Results section.*

NMR
Coupling
Constants		 Thermal
Unfolding of
Two Small
Proteins		 Reversible
Folding of an
α-Helical
Peptide		 Reversible
Folding of a
β-Hairpin
Peptide		 Polymeric
Behavior of
Polyglutamine
Rigid 0% / 0% / 1% 5% 10% 5%
Body (90%, 5Å,
60°)		 (75%, 2.5Å,
25°)		 (50%, 2.0Å,
10°)		 (50%, 2.0Å,
10°)		 0%
Sidechain
(χi, χj) 		0% / 25% /
24.8%
(2x, 60%, 30°)		 14.3%
(2x, 60%,
30°)		 9%
(2x, 60%,
30°)		 28.5%
(3x, 60%,
30°)		 30%
(4x, 60%, 30°)
Pivot
(ϕ,ψ) 		90% / 67.5% /
66.8%
(70%, 10°)		 65.2%
(70%, 10°)		 58.3%
(70%, 10°)		 47.9%
(70%, 10°)		 37.8%
(70%, 10°)
Omega
(ω) 		10% / 7.5% /
7.4%
(85%, 5°)		 11.5%
(85%, 5°)		 6.5%
(90%, 5°)		 5.3%
(90%, 5°)		 4.2%
(90%, 5°)
Concerted
Rotations
Four (ϕ,ψ)
pairs in
concert 		0% / 0% / 0% 4% 16.2% 13.3% 28%
*

The first column lists the degrees of freedom sampled by a particular type of move. Rigid-body moves are always coupled and sample global rotational and translational degrees of freedom. These moves are especially important for the simulations of the two proteins, the FS peptide, and “trpzip1”, because the droplet consists of the polypeptide, neutralizing counterions, and excess salt. The concerted rotation approach124 samples four consecutive sets of backbone ϕ, ψ angles. The second through fifth columns give the frequencies (in percent) with which the specific move type (row element) is picked for each system. There are three separate values listed for the coupling constant work, which are for alanine (no χ-angles), net neutral dipeptides, and net charged dipeptides, respectively. Additional information is given in parentheses, indicating what portion of the moves of a certain type consists of stepwise perturbations of the respective degree(s) of freedom, along with the maximum step size. The remaining fraction consisted of moves fully randomizing the respective degree(s) of freedom. In addition, due to their low computational complexity, sidechain moves consist of multiple identical cycles indicated by the first entry in parentheses.