Debanjan Sen,PhD

i installed the packages mentioned in installation documentation. and the updated error given bellow PS C:\Users\HP\Downloads> pip install mdtraj Collecting mdtraj Using cached mdtraj-1.9.7.tar.gz (2.1 MB) Installing build dependencies ......

Sir, My gromacs folder present in /usr/local/bin I thought (cd /md/root/dir, plumed patch -p) sudo may be required to patch MD engine so used sudo.. cd /md/root/dir, for the root...

After executing sudo make install it return following errors cd install/python && rm -fr *.so plumed.cpp build && \ unset CXX && unset CC && unset CFLAGS && unset CXXFLAGS...

[image: image.png] unable to open the given page. On Sun, Sep 11, 2022 at 11:55 PM Moritz Hoffmann ***@***.***> wrote: > Hi, have you activated the correct environment before starting...

#after exploring the tutorial section I did the following things 1. conda activate pyemma to activate the env in side the working folder 2. conda activate pyemma jupyter nbextension enable...

i think issues are associated with nglview..

#**In the tutorial i found file = mdshare.fetch('hmm-doublewell-2d-100k.npz', working_directory='data') or pdb = mdshare.fetch('alanine-dipeptide-nowater.pdb', working_directory='data') files = mdshare.fetch('alanine-dipeptide-*-250ns-nowater.xtc', working_directory='data') print(pdb) print(files) I have three 100ns gromacs MD trajectory entitled md_100ns-0.xtc,md_100ns-1.xtc,md_100ns-2.xtc and...

%matplotlib inline import matplotlib.pyplot as plt import numpy as np import mdshare import pyemma # for visualization of molecular structures: import mdtraj from threading import Timer from pyemma import *...

files=pyemma.coordinates.source("md_100.xtc",top="md_100.pdb") print(files) output:- feat = pyemma.coordinates.featurizer(files) ---------------------------------------------------------------------------ValueError Traceback (most recent call last)~\AppData\Local\Temp/ipykernel_5568/3492995895.py in ----> 1 feat = pyemma.coordinates.featurizer(files) C:\ProgramData\Miniconda3\envs\pyemma\lib\site-packages\pyemma\coordinates\api.py in featurizer(topfile) 142 """ 143 from pyemma.coordinates.data.featurization.featurizer import MDFeaturizer--> 144 return...

:( Downgrading to ipywidgets 7 would help.??