Stack Overflow
Stack Overflow

Questions tagged [mdanalysis]

MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories. It allows one to read molecular dynamics trajectories and access the atomic coordinates through NumPy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. Fairly complete atom Selection Commands are implemented. Trajectories can also be manipulated and written out in a range of formats.

MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, Amber, NAMD, or LAMMPS; it also reads other formats. It can write most of these formats, too, together with atom selections for use in Gromacs, CHARMM, VMD and PyMol.

It allows one to read molecular dynamics trajectories and access the atomic coordinates through NumPy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. Fairly complete atom Selection Commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out in a range of formats.

37 questions
1
vote
1 answer

Question about Using MDAPackmol (packmol in python)

I would like to use the python wrapper for packmol (MDAPackmol) for my research. In order to do so, I have tried to work with the example code and pdb files provided on GitHub so I can gain an understanding of the how to use the wrapper. However,…
bioinf99
  • 11
  • 4
1
vote
1 answer

Time series data for water molecules from its dcd file

I am trying to make a file which contain time series data of water molecules from dcd file. Is it possible to generate this data using any of MDAnalysis module or function? Or is there any python script to generate this file? I need to generate this…
iqra khan
  • 45
  • 1
  • 6
1
vote
2 answers

Extracting one chain from MD trajectory file using MDAnalysis

I would like to extract one chain from my molecular dynamics trajectory (xtc file) using MDAnalysis. I expected it to be very simple, but an error occurred and I am not sure why I am getting it. Here is the code: import MDAnalysis as mda u =…
HungryMolecule
  • 195
  • 11
1
vote
1 answer

problem with python: undefined symbol: sqmI

i have installed on my Ubuntu, this package: pyinteraph.py after the installation, i have this problem: File "/home/user/Scrivania/PyInteraph-1.0/test/pyinteraph/pyinteraph", line 162, in from libinteract import libinteract as li File…
Pietro Delre
  • 13
  • 5
1
vote
1 answer

PCA using MDAanalysis (python3.7)

I started to work in the field of computational chemistry and I was ask to do Principal Component Analysis on some trajectory from molecular dynamics. I was told to use MDAnalysis package, thus I find one tutorial on their page a tried to follow it…
HungryMolecule
  • 195
  • 11
1
vote
1 answer

Python / MDAnalysis SelectionError: Selection failed: 'could not convert string to float

I'm new to Python and MDAnalysis. I am trying to use MDAnalysis for analysis. However, I run into this error: SelectionError: Selection failed: could not convert string to float 'cold'. I would like to select the molecules named "BF4", "EMI",…
Candy Deck
  • 13
  • 4
1
vote
2 answers

How to use MDAnalysis to principal_axes and moment_of_inertia with a group of atoms?

I am trying to use MDAnalysis (MDAnalysis.__version__ == 0.17.0) API functions principal_axes() and moment_of_inertia() to calculate these matrices for a group of selected atoms as described in the doc: import MDAnalysis from…
0x90
  • 39,472
  • 36
  • 165
  • 245
1
vote
0 answers

close Universe in MDAnalysis module

Is it possible to close or unload a Universe in MDAnalysis module? I didn't find any such function on MDAnalysis pages I want to modify the trajectory with another module and then load it again in MDAnalysis, but I get a following: File…
user4770892
1
vote
1 answer

Remove a version of a python package

I'm trying to install a Python package name MDAnalysis which required numpy. The problem is the default path for python is /System/Library/Frameworks/Python.framework/Versions/2.7/lib/ but my package (installed with pip) was in: …
pomxipum
  • 315
  • 1
  • 3
  • 9
1
vote
1 answer

How to use pickle to dump a universe object from MDAnalysis module?

I tried to use pickle to dump a MDAnalysis.universe object, but I got error mmessage like Traceback (most recent call last): File "convert.py", line 9, in blob = pickle.dumps(u) File "/usr/lib/python2.7/pickle.py", line 1374, in…
DistributedSlacker
  • 45
  • 5
0
votes
1 answer

Regarding tau_max in Survival Probability calculation using MDAnalysis python package

I am newbie in using MDAnalysis as well as python in general. I have performed a 100 ns simulation on a protein and wanted to calculate the survival probability of my water molecules within my selection. The thing is using the given code of…
Alvea Tasneem
  • 11
  • 2
0
votes
0 answers

I have a DX file containing PME data, I want to plot an average potential profile through python code

I have a DX file containing PME data, I want to plot an average potential profile through python code. Can anyone please help with the code I do not know how to write a python code for the same
Coldy_14
  • 1
0
votes
0 answers

Iterating over molecules from LAMMPS dumpfile using MDAnalysis

I have a Lammps Dumpfile in the format "id mol type xu yu zu", where id is the ID of each molecule and mol is the ID of each molecule (atoms connected by a bond). import MDAnalysis as mda from MDAnalysis.transformations import…
ludwig_boltzplatz
  • 21
  • 3
0
votes
0 answers

Why is the curve fitting in MDAnalysis persistence length not working?

I'm trying to find the persistence length of a polymer from a LAMMPS simulation using the polymer analysis module in MDAnalysis. However, the persistence length seems to only return 1.0 no matter which data set I give it, and the graph of the curve…
Peggy Brooks
  • 1
  • 1
0
votes
1 answer

MDAnalysis how to index the charge?

I have been trying to figure out this process that is very dependent on the charge. However, I am finding that, for waters, I am getting a value not equal to 0 for the sum of a water molecule charge. To investigate this, I wanted to compare the…
Confused_scientist
  • 37
  • 4
1
2
3