The following list contains descriptions of biases developed for the PLUMED-SASA module. They can be used in combination with other biases outside of the SASA module.

Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. The atoms for which the SASA is desired should be indicated with the keyword ATOMS, and a pdb file of the protein must be provided in input with the MOLINFO keyword. The algorithm described in [62] is used for the calculation. The radius of the solvent is assumed to be 0.14 nm, which is the radius of water molecules. Using the keyword NL_STRIDE it is also possible to specify the frequency with which the neighbor list for the calculation of SASA is updated (the default is every 10 steps).

Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. The atoms for which the SASA is desired should be indicated with the keyword ATOMS, and a pdb file of the protein must be provided in input with the MOLINFO keyword. The LCPO algorithm is used for the calculation (please, read and cite [135]). The radius of the solvent is assumed to be 0.14 nm, which is the radius of water molecules. Using the keyword NL_STRIDE it is also possible to specify the frequency with which the neighbor list for the calculation of the SASA is updated (the default is every 10 steps).