Table 1:
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 |
Natoms is number of atoms in the simulation systems.
GaMD_Dih and GaMD_Dual represent the dihedral and dual-boost GaMD simulations respectively.
ΔVavg and
σΔV are the average and standard deviation of the GaMD boost potential.