vermouth.rcsu.go_vs_includes module

class vermouth.rcsu.go_vs_includes.VirtualSiteCreator[source]

Bases: Processor

Create virtual-sites for the Martini Go model implementation or the specific water biasing options.

See vermouth.rcsu for more details.

Every molecule must have a moltype name under the “moltype” key of the molecule meta.

See also

NameMolType

Assign molecule type names to the molecules in a system.

add_virtual_sites()

add_virtual_sites(molecule, prefix, backbone='BB', atomname='CA', charge=0)[source]

Add the virtual sites for GoMartini in the molecule.

One virtual site is added per backbone bead of the the Martini protein. Each virtual site copies the resid, resname, and chain of the backbone bead. It also copies the reference to the position array, so the virtual site position follows if the backbone bead is translated. The virtual sites are added after all the other atoms of the molecule, each in its own charge group, with “CA” as atomname, and a charge of 0. The atomname and charge can be set with the atomname and charge argument, respectively.

The bead type of the virtual sites is names “<prefix>_<resid>”. Where prefix is provided as an argument of the function, and is expected to be the molecule type name.

Parameters:

  • molecule (vermouth.molecule.Molecule) – The molecule to augment with virtual sites.

  • prefix (str) – The prefix to use for bead type names. Usually the molecule type name.

  • backbone (str) – The atomname of the backbone beads.

  • atomname (str) – The atomname of the virtual sites.

  • charge (float or int) – The charge of the virtual sites.

run_molecule(molecule)[source]
run_system(system)[source]