Skip to main content
. Author manuscript; available in PMC: 2021 Aug 1.
Published in final edited form as: Biochim Biophys Acta Gen Subj. 2020 Apr 13;1864(8):129615. doi: 10.1016/j.bbagen.2020.129615

Table 1:

Summary of GaMD simulations performed on the adenosine A1 receptor (A1AR).

System aNatoms Dimension(Å3) Program bMethod Simulation cΔVavg (kcal/mol) dσΔv (kcal/mol)
ADO-A1AR-Gi 180,394 93x111x167 NAMD GaMD_Dih 300 ns × 2 5.04 2.22
GaMD_Dual 300 ns × 2 10.14 2.59
ADO-A1AR-Gi 180,394 93x111x167 AMBER GaMD_Dih 300 ns × 3 6.89 4.06
GaMD_Dual 300 ns × 3 21.43 6.50
ADO-A1AR-GiVCP171 180,403 93x111x167 AMBER GaMD_Dih 300 ns × 3 6.80 2.74
GaMD_Dual 300 ns × 3 24.80 6.61
a

Natoms is number of atoms in the simulation systems.

b

GaMD_Dih and GaMD_Dual represent the dihedral and dual-boost GaMD simulations respectively.

c

ΔVavg and

d

σΔV are the average and standard deviation of the GaMD boost potential.