vermouth.processors.water_bias module

class vermouth.processors.water_bias.ComputeWaterBias(auto_bias, water_bias, idr_regions)[source]

Bases: Processor

Processor which computes the water bias for the Martini Go and Martini IDP model.

The water bias strength is defined per secondary structure element in water_bias and assigned if auto_bias is set to True. Using the idr_regions argument the water_bias can be changed for intrinsically disordered regions (IDRs). The IDR bias superseeds the auto bias.

This Processor updates the system.gmx_topology_params attribute.


If the procedure by which to assign the water bias is to be changed this processor is best subclassed and the assign_residue_water_bias method overwritten.

param auto_bias:

apply the automatic secondary structure dependent water biasing

type auto_bias:


param water_bias:

a dict of secondary structure codes and epsilon value for the water bias in kJ/mol

type water_bias:

dict[str, float]

param idr_regions:

regions defining the IDRs

param prefix:

prefix of the Go virtual-site atomtypes

type prefix:


param system:

the system of the molecules is used for storing the nonbonded parameters

type system:


assign_residue_water_bias(molecule, res_graph)[source]

Assign the residue water bias for all residues with a secondary structure element or that are defined by the region selector. Region selectors supercede the auto assignment.


Assign water bias for a single molecule


Assign the water bias of the Go model to file. Biasing is always molecule specific i.e. no two different vermouth molecules can have the same bias.


system (vermouth.system.System)