. Author manuscript; available in PMC: 2013 Nov 13.

Published in final edited form as: J Chem Theory Comput. 2012 Oct 11;8(11):4413–4424. doi: 10.1021/ct300696c

Table 2.

Summary of system size, simulation time, and MD methods used of folding simulations performed in this work.

System	Number of water molecules	Time (μs)^b	MD methods
Dipeptide^a	550	0.05	REMD^c
AK17	1600	0.2	REMD
Fs	1850	0.2	REMD
	1850	3.0	MD
GB1p	1700	0.75	REMD
D47P	1700	0.35	REMD
	1800	1.3; 2.1; 3.5	MD
GB1m2	1700	0.35	REMD
Trp-cage	1800	0.2	REMD
	1800	3; 3	MD
BBA5	1800	0.5	REMD
	1800	8; 8	MD
α3D	4500	10; 20; 30	MD

REMD simulations were carried out for all 20 natural amino acids.

For REMD simulations, the simulation time of each replica is listed. For standard MD simulations, the simulation time of each run is listed. Simulation times of multiple runs are all listed, separated by semi-colons.

Each REMD involved has 18 replicas with associated temperatures ranging from 300 K to 480 K.