sbhakat

For example I don't need range. I just want absolute values of three atoms. So if my atom numbering in .pdb file starts goes like 5, 8,10 should it be...

Hi Team Loos, Currently Plumed supports calling analysis packages such as MDAnalysis or MDtraj to design collective variables. One can call MDAnalysis as follows: ``` MOLINFO STRUCTURE=helix.pdb PYTHON_BIN=python g1: GROUP...

Thanks @gph82 . It definitely needs a new release. It will be great to have an .yml file which contains the information about software versions so that the users doesn't...

But I can call the following code `from vde_metadynamics import *`

Also when I try to print the tiCA components they look something like following. Seems something is wrong 

Yes I have two tICS and 2 features. But in wwdomain case it seems like you provide the tIC data as a training set `train_tica_data = [tica_data[i][::1,:2] for i in...

When running this getting the following error `train_tica_data = [tica_data[i][::1,:2] for i in tica_data.keys()] concat_train_data = np.concatenate([tica_data[i][::1,:2] for i in tica_data.keys()])` Error --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) in...

Gives an error like --------------------------------------------------------------------------- TypeError Traceback (most recent call last) in () ----> 1 train_tica_data = [ i[::1,:2] for i in tica_data] 2 concat_train_data = np.concatenate([ i[::1,:2] for i...

Okay I got this crazily huge Plumed input file but there are some questions There is existence of ARG=l0_0,l0_1 but where does in the script it is defined? I think...

Also I think for a big protein driving on all these networks will be craziness. I guess driving on the first network is a good try? What do you think?