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. Author manuscript; available in PMC: 2018 Apr 30.
Published in final edited form as: Annu Rep Comput Chem. 2017 Aug 10;13:231–278. doi: 10.1016/bs.arcc.2017.06.005
igamd Flag to apply boost potential
= 0 (default) no boost is applied
= 1 boost on the total potential energy only
= 2 boost on the dihedral energy only
= 3 dual boost on both dihedral and total potential energy
iE Flag to set the threshold energy E
= 1 (default) set the threshold energy to the lower bound E = Vmax
= 2 set the threshold energy to the upper bound E = Vmin + (Vmax - Vmin)/k0
ntcmd The number of initial conventional molecular dynamics simulation steps used to calculate the maximum, minimum, average and standard deviation of the system potential energies (i.e., Vmax, Vmin, Vavg, σV). The default is 1,000,000 for a simulation with 2 fs timestep.
nteb The number of simulation steps used to equilibrate the system after adding boost potential. The default is 1,000,000 for a simulation with 2 fs timestep.
sigma0P The upper limit of the standard deviation of the total potential boost that allows for accurate reweighting if igamd is set to 1 or 3. The default is 6.0 (unit: kcal/mol).
sigma0D The upper limit of the standard deviation of the dihedral potential boost that allows for accurate reweighting if igamd is set to 2 or 3. The default is 6.0 (unit: kcal/mol).