alchemlyb.parsing.gmx.rst

Gromacs parsing

alchemlyb.parsing.gmx

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 ~alchemlyb.estimators.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 ΔH 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

alchemlyb.parsing.gmx.extract_u_nk

alchemlyb.parsing.gmx.extract