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. Author manuscript; available in PMC: 2019 Apr 5.
Published in final edited form as: Expert Opin Drug Discov. 2018 Oct 29;13(11):1055–1065. doi: 10.1080/17460441.2018.1538207

Table 1:

Parameters of GaMD simulations performed on drug binding to target receptors.

Systema Program Boostb cMD (ns) GaMD Equilibration (ns) GaMD Production (ns)
HIV Protease AMBER Dual 10 50 2500, 2500, 2436, 2434, 1445, 500, 500, 500, 500, 500
M2-QNB AMBER Dual 10 50 400, 400, 400
M2-ARC AMBER Dual 10 50 2030, 1520, 1190, 650, 650, 650, 620, 600, 600, 540
M2-IXO AMBER Dual 10 50 1050, 1000, 940, 500, 500, 500, 500, 480, 450, 410
M3 NAMD Dual 10 50 400, 300, 300
A1AR AMBER Dual 2 50 500, 500, 500, 500, 500
NAMD Dual 2 50 300, 300, 300, 300, 300
NAMD Dihedral 2 50 200, 200, 200, 200, 200
a

QNB is the 3-quinuclidinyl-benzilate inverse agonist, ARC is the arecoline partial agonist and IXO is the iperoxo full agonist of the M2 muscarinic receptor.

b

The “Dual” and “Dihedral” stand for dual-boost and dihedral-boost GaMD simulations, respectively.