pygromos.gromos.pyGromosPP package¶
Submodules¶
pygromos.gromos.pyGromosPP.com_top module¶
COM_TOP
Python version of the GROMOS++ program to combine two topologies. All molecules are combined to a single topology and it can be decided where the solvent and parameters ar taken from.
This mehod can also be called directly via top1.com_top(top2), top1 + top2 or top1+=top2
Author: Marc Lehner
- pygromos.gromos.pyGromosPP.com_top.com_top(top1: pygromos.files.topology.top.Top, top2: pygromos.files.topology.top.Top, topo_multiplier: List[int] = [1, 1], solvFrom1: bool = True, paramFrom1: bool = True, verbose: bool = True) pygromos.files.topology.top.Top[source]¶
Python version of the GROMOS++ program to combine two topologies. All molecules are combined to a single topology and it can be decided where the solvent and parameters ar taken from.
This mehod can also be called directly via top1.com_top(top2), top1 + top2 or top1+=top2
Author: Marc Lehner
- Parameters
top1 (Top) – a topology
top2 (Top) – another topology
topo_multiplier (List[int]) – multiplier for topos. entries must be >=0
solvFrom1 (bool, optional) – wether to take the solvent from topology 1, by default True
paramFrom1 (bool, optional) – wether to use topo1 as main, by default True
verbose (bool, optional) – additional proints for information, by default True
- Returns
combined topology
- Return type
pygromos.gromos.pyGromosPP.ran_box module¶
Python implementation of the Gromos++ program ran_box which is used to generate randomized configurations for liquids (and gases)
Author: Marc Lehner
- pygromos.gromos.pyGromosPP.ran_box.ran_box(in_top_path: str, in_cnf_path: str, out_cnf_path: str = '', periodic_boundary_condition: str = 'r', nmolecule: int = 1, dens: float = 1.0, threshold: Optional[float] = None, layer: bool = False, boxsize: Optional[float] = None, fixfirst: bool = False, seed: Optional[float] = None, _binary_name: str = 'ran_box', verbose: bool = True, return_command_only: bool = False) str[source]¶