mdtraj | open library for the analysis of molecular dynamics
kandi X-RAY | mdtraj Summary
kandi X-RAY | mdtraj Summary
Read, write and analyze MD trajectories with only a few lines of Python code. With MDTraj, you can. For details, see the website at mdtraj.org. To get involved, take a look at the github issue tracker and/or the gitter room. MDTraj is research software. If you make use of MDTraj in scientific publications, please cite it. The BibTeX reference is. GNU LGPL version 2.1, or at your option a later version of the license. Various sub-portions of this library may be independently distributed under different licenses. See those files for their specific terms.
Support
Quality
Security
License
Reuse
Top functions reviewed by kandi - BETA
Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of mdtraj
mdtraj Key Features
mdtraj Examples and Code Snippets
Community Discussions
Trending Discussions on mdtraj
QUESTION
I understand the question is not appropriate for this platform, but I can try if I can get some hints,
I've been trying to plot the free energy landscape of a protein structure ("Chignolin"). I'm completely run out of ideas how to do that!! I've MD simulation trajectory file Trajectory file and using pyemma to plot the energy landscape. But I'm getting the error "" TypeError: plot_free_energy() takes from 2 to 20 positional arguments but 28 were given ""
Could someone figure out where the problem lies? Here is my code
...ANSWER
Answered 2021-Feb-10 at 17:53I recommend you start reading the documentation, especially the "learn PyEMMA" section containing Jupyter notebooks teaching you the work-flow to extract properly weighted "pseudo" free-energy surfaces. Usually these surfaces are drawn into the dimensions of the first two slowest dynamical processes, but you can think of any other combination as well. These dimensions are defined by a TICA or VAMP projection, which are basically methods to extract the slow modes from your data, in case of proteins this contains folding and rare events.
As a primer I suggest reading this tutorial first, as it gives you a brief overview how to load and process your data to extract the slow modes. Note that this not yet contain Markov state modelling, so read further in the other examples to learn about that.
QUESTION
I want to print all atoms except H (hydrogen) from the pdb file. Here is the file
https://github.com/mahesh27dx/molecular_phys.git
Following code prints the objects of the file
...ANSWER
Answered 2020-Dec-01 at 01:04You can do the following:
QUESTION
I am working on a project which uses the CircleCI continuous integration platform. I use Python as main language and Miniconda as platform. I want to test multiple Python and NumPy versions using Miniconda on CircleCI.
I tried to use different Python images but it uses only Python 3.7 as I install the latest Miniconda version. Could you tell me how to use multiple versions?
Below is config.yml
:
ANSWER
Answered 2019-Oct-09 at 10:52Here is a minimal example configuration on how to use CircleCI with Miniconda and specific Python and NumPy versions, starting with an empty ubuntu:bionic
image.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install mdtraj
Support
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesStay Updated
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page