GaMD-GENESIS: Manual

Simulation Parameter Settings

gamd YES / NO
Default : NO
Enable the GaMD method.

boost YES / NO
Default : YES
Flag to apply GaMD boost to the system. If boost = NO, boost is not applied but GaMD parameters are updated from the trajectory.

boost_type DUAL / DIHEDRAL / POTENTIAL
Default: DUAL
Type of boost.
DUAL: Boost is applied on both the dihedral and total potential energies.
DIHEDRAL: Boost is applied on only the dihedral energy.
POTENTIAL: Boost is applied on only the total potential energy.

thresh_type LOWER / HIGHER
Default: LOWER Type of threshold.
LOWER: E is set to the lower bound E = Umax.
HIGHER: E is set to its upper bound E = Umin + 1/k.

update_period Integer
Default: 0
Period of updating parameters in units of time step.

sigma0_pot Real
Default: 6.0 (unit: kcal/mol)
Upper limit of the standard deviation of the total potential boost that allows for accurate reweighting.

pot_max Real
Default: -99999999.0 (unit: kcal/mol)
Maximum of the total potential energy of the system.

pot_min Real
Default: 99999999.0 (unit: kcal/mol)
Minimum of the total potential energy of the system.

pot_ave Real
Default: 0.0 (unit: kcal/mol)
Average of the total potential energy of the system.

pot_dev Real
Default: 0.0 (unit: kcal/mol)
Standard deviation of the total potential energy of the system.

sigma0_dih Real
Default: 6.0 (unit: kcal/mol)
Upper limit of the standard deviation of the dihedral boost that allows for accurate reweighting.

dih_max Real
Default: -99999999.0 (unit: kcal/mol)
Maximum of the dihedral energy of the system.

dih_min Real
Default: 99999999.0 (unit: kcal/mol)
Minimum of the dihedral energy of the system.

dih_ave Real
Default: 0.0 (unit: kcal/mol)
Average of the dihedral energy of the system.

dih_dev Real
Default: 0.0 (unit: kcal/mol)
Standard deviation of the dihedral energy of the system.

NOTE: Please refer to the GENESIS user manual for more detailed description.

Reference

H. Oshima, S. Re, Y. Sugita, Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules. J Chem Theory Comput 15, 5199-5208 (2019).