colvar module
Code author: Niklaus Johner <niklaus.johner@a3.epfl.ch>
This module is a collection of functions to work in conjunction with namd’s colvar module.
It mainly contains functions to read som of the files output by namd.
-
ReadNamdSMDFile(filename)[source]
This function opens and reads a namd ouput file
It looks for the SMD ouput and returns it in a dictionary
with keys [‘timestep’,’cm_pos’,’force’]
-
IntegrateFloatList(x_list, y_list, lim=-1)[source]
Function to integrate a FloatList y over x
from x_list[0] to x_list[lim]
-
ReadColvarFile(filename, skip_first_n=1)[source]
This function opens and reads a namd colvar trajectory file
It searches for the fields in the first line of the file and then generates
a dictionary with these fields as keys