Gromacs parsing¶
Parsers for extracting alchemical data from Gromacs output files.
The parsers featured in this module are constructed to properly parse XVG files containing Hamiltonian differences (for obtaining reduced potentials, \(u_{nk}\)) and/or Hamiltonian derivatives (for obtaining gradients, \(\frac{dH}{d\lambda}\)).
To produce such a file from an existing EDR energy file, use gmx energy -f <.edr> -odh dhdl.xvg with your installation of Gromacs.
If you wish to use FEP-based estimators such as MBAR that require reduced potentials for all lambda states in the alchemical leg, you will need to use these MDP options:
calc-lambda-neighbors = -1 ; calculate Delta H values for all other lambda windows
dhdl-print-energy = potential ; total potential energy of system included
In addition, the full set of lambda states for the alchemical leg should be explicitly specified in the fep-lambdas option (or coul-lambdas, vdw-lambdas, etc.), since this is what Gromacs uses to determine what lambda values to calculate \(\Delta H\) values for.
To use TI-based estimators that require gradients, you will need to include these options:
dhdl-derivatives = yes ; write derivatives of Hamiltonian with respect to lambda
Additionally, the parsers can properly parse XVG files (containing Hamiltonian differences and/or Hamiltonian derivatives) produced during expanded ensemble simulations. To produce such a file during the simulation, use gmx mdrun -deffnm <name> -dhdl dhdl.xvg with your installation of Gromacs.
To run an expanded ensemble simulation you will need to use the following MDP option:
free_energy = expanded ; turns on expanded ensemble simulation, lambda state becomes a dynamic variable
API Reference¶
This submodule includes these parsing functions:
- alchemlyb.parsing.gmx.extract_dHdl(xvg, T)¶
Return gradients dH/dl from a Hamiltonian differences XVG file.
- alchemlyb.parsing.gmx.extract_u_nk(xvg, T)¶
Return reduced potentials u_nk from a Hamiltonian differences XVG file.