Gromacs variables

Some parameters in force fields included in the Vermouth library make use of Gromacs preprocessing.

Preprocessing statements in gromacs mdp files may be used to customise topologies at the preprocessing stage of simulation setup. The statements in the define statement of the input molecular dynamics parameters (.mdp) file are passed to the topology file, where #ifdef statements are used to modify the exact topology of the molecule. For more examples of #ifdef statements, see the gromacs manual.

Note that the define statement in the .mdp file is only given once, with arguments delineated by the -D prefix on the same line.

FLEXIBLE

The FLEXIBLE defines is used to switch some bonds between harmonic bonds and constraints. This is important for minimization purposes. Flexible bonds are activated through the .mdp file using:

define = -DFLEXIBLE

POSRES

The POSRES defines is used to activate any position restraints defined in system topologies. Position restraints are applied to beads by Martinize2 via the -p flag. Position restraints may be useful for minimization and equilibration purposes. Position restraints are applied to the system using:

define = -DPOSRES

POSRES_FC

For minmization and equilibration purposes, it may be useful to reduce the position restraint on a molecule across several successive simulations. In Martinize2, the strength of the position restraint is controlled by the -pf flag, and is 1000 kJ/mol/nm^2 by default. However, as position restraints are written as a ifndef statement in topology files, its exact value can be passed from the mdp file. For example:

define = -DPOSRES -DPOSRES_FC=500

will reduce the position restraint to 500 kJ/mol/nm^2 directly.