Calculate NMR relaxation time from molecular dynamics trajectory file
Project description
NMRforMD is a python script to calculate NMR relaxation times from molecular dynamics trajectory files. Used in combination with MDAnalysis, it allows for the analysis of trajectory files from LAMMPS, GROMACS, or AMBER simulation package.
Information
NMRforMD is in development and likely to return errors. Please raise an issue here if you find one.
For details and a tutorial, have a look at the documentation.
Installation
Using pip, type in a terminal:
pip install nmrformdOr, clone this repository on your computer and use pip from the main directory:
git clone git@github.com:simongravelle/nmrformd.git
cd nmrformd/
pip install .You can run the test using pytest:
cd tests
pytest mytest.pyBasic example
This is an example showing how to use NMRforMD to measure NMR signal from a molecular dynamics simulations. See the tutorial for more information.
import MDAnalysis as mda
import nmrformd
u = mda.Universe("topology.tpr", "trajectory.xtc")
nmr_result = nmrformd.NMR(u, "type H", "type H", "full", 0, "m0")The NMR relaxation time T1 is given by nmr_result.T1.
Known issues
for very large trajectory file, the code requires a lot of memory
currently only residues have been tested
the code has mostly been tested with GROMACS trajectory file
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