15
votes
Visualizing MD generated electron density cubes as trajectories
Jmol is completely capable to do what you want. It reads cube file format and works with scripts. Take a look at this link related to making movies.
The idea is:
...
- 22.3k
15
votes
Accepted
How can I use a GUI on a supercomputer?
I prefer to just download the data from the remote disks and then do the plots on my own local machine, which has all of my favorite tools for post-processing my data.
I understand that this can be ...
- 33.5k
14
votes
How can I visualize the trajectory of a VASP simulation?
ASE
You can use ASE environment to visualize, it has different options as well. e.g., you can use this command: ase gui vasprun.xml
- 1,426
13
votes
What is the most user friendly software for frequency visualization rendering?
VMD Normal Mode Wizard
If you're goal is to create high quality visualizations of vibrations I recommend VMD. It's highly customizable in terms of colors, resolution, and representation.
The setup ...
- 7,957
13
votes
Accepted
Molden installation on macOS?
I believe that these instructions from this YouTube video "How to install Molden on Mac (OS X High Sierra)" work well
For some reason the "ftp" button on Molden's website is broken however, the <...
- 7,957
13
votes
9 x 9 x 9 periodic xyz file to cif file format
You can use for example pymatgen in python to do this. The tricky part of your question is to find a unit cell in step 2.
I outline the steps here:
Read your xyz file into a pymatgen structure.
Use ...
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13
votes
Accepted
How to separate the data plot for spin up and spin down band structure into 2 different graphs, in Pymatgen?
Here I provide an example with my own python scripts to realize your purpose rather than using Pymatgen (You can save data firstly with Pymatgen and plot with python). I assume that you can perform ...
- 14.9k
13
votes
How can I use a GUI on a supercomputer?
It would probably be easier to use some software such as WinSCP. It allows you to select the location on your remote system and synchronise with the local system by matching either the time stamp or ...
- 2,603
12
votes
Plotting of natural bond orbitals (NBOs)
NBO 7.0
The program NBO 7.0 seems to be quite well maintained, with version 7.0.9 released fewer than 30 days ago.
Advantages:
Has interfaces to ADF, DEMON2K, FIREFLY/PC-GAMESS, GAMESS(US), GAUSSIAN, ...
- 33.5k
12
votes
Accepted
3D Visualization of Molecule / Surface by 3D Model (.stl)
OpenBabel
This masterpiece of software can convert between a huge amount of different file formats.
The mains site can be accessed here.
In my Linux box running OpenBabel 3.0.0, the commands for ...
- 22.3k
11
votes
Accepted
How to create a Potential Energy Surface in Chemcraft?
I am the author of Chemcraft. Your job contains a 2-dimensional PES scan, and currently Chemcraft can visualize only 1-dimensional scans. I plan to implement support of 2d scans in future. It is ...
- 406
11
votes
What are good tools for visualizing glide planes and screw axes?
Jmol/JSmol
Did you consider Jmol/JSmol? It is freely available for Windows / Mac / Linux, scriptable, may export what is being displayed in formats relevant to chemistry (e.g., .pdb, .sdf), as image (...
- 1,579
11
votes
How to create a 3D band structure from DFT band structure calculation?
Consider a graphene Hamiltonian, whose dispersion looks a lot like the one in your figure. Per these notes, its k-space Hamiltonian may be written as:
$$
H(k)=-t \sum_{\delta} [\cos(k\cdot\delta)\...
- 2,281
10
votes
Molecular visualization software in Jupyter (IPython) Notebooks
NGLVIEW
I discovered it very recently when I was using MDAnalysis to play with molecular dynamic trajectories. Therefore, I am not able to write about pros/cons.
Site: https://github.com/nglviewer/...
- 22.3k
10
votes
Accepted
Why the Open Babel submenu is faded out in Avogadro 2 and I can't optimize geometry in Mint 20?
Solution: Install Open Babel
The underlying cause is that Open Babel was not installed by default as a dependency of Avogadro 2. I think this is odd, as basic features like geometry optimization ...
- 4,048
10
votes
Plotting of natural bond orbitals (NBOs)
ADF
With the Amsterdam Modeling Suite you can calculate (ADF, DFTB) and plot NBOs in the graphical user interface within the same package.
Here's an example applied to NMR analysis.
Here's one ...
- 101
10
votes
Accepted
How to map the electrostatic potential from GAUSSIAN, on a solvent accessible surface?
The Jmol software is able to plot different surfaces.
In the example below, the system is a Mobius strip and the ESP was calculated using MOPAC but as Jmol is full compatible with Gaussian outputs, I ...
- 22.3k
10
votes
How to create a 3D band structure from DFT band structure calculation?
VASPKIT
VASPKIT offers a tool to plot 3D band structure using VASP. The method select K-path on a surface of the Irreducilbe Brillouin zone and calculate the K-dependent band energies on those K-...
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10
votes
Accepted
Best software to plot Charge densities
I am going to agree with Camps here, but I should add to this that you can do a composite approach to making a figure such as this one. You should follow a procedure as such.
Calculate the charge ...
- 10.8k
9
votes
What is the most user friendly software for frequency visualization rendering?
Jmol
The Jmol package is able to do what you want. You can produce the animations below just using point & click with your mouse.
But you can also use its scripting capabilities to work with batch ...
- 22.3k
9
votes
Software to draw 3d micelle configuration
I found some software that can do this kind of work:
Rhino3d
3ds Max
- 339
9
votes
How to automatically plot atomic structures with magnetic moments?
This took some digging, but I can supply at least a partial answer.
Assuming you can copy the list of magnetic moments to a list, you could trick whatever software you are using for visualization into ...
- 10.8k
9
votes
Great computer graphics for matter modelling
Magnetic Anisotropy
The best way to understand magnetic anisotropy is to visualize it. I think a visualization should be co-produced with every calculation of magnetic anisotropic energy.
The ...
- 8,922
9
votes
Plotting of natural bond orbitals (NBOs)
Q-Chem + Jmol
The combination of Q-Chem and Jmol seems to work well (but is not yet well documented).
Q-Chem
In the Q-Chem input file one has to put
...
- 1,431
9
votes
Accepted
How to make the input generator plugin work in Avogadro 2 on GNU/Linux?
tldr; they need to be in certain directories to be found.
I don't know why the input generators were not part of the install package. Certainly on Mac, and AFAIK on Windows, they are and should be. On ...
- 9,045
9
votes
Accepted
How can I visualize the trajectory of a VASP simulation?
VMD
I had to dig up the VMD script that I used for this. VMD doesn't detect the file type automatically, so you have to tell it to use VASP_XDATCAR5.
In the VMD Tk ...
- 1,901
9
votes
Structure visualization software for Windows
You can install xcrysden using Xming and Cygwin without resorting to WSL and it worked well for me.
Install XMing and RUN
Install CYGWIN with the following packages:
...
- 4,428
9
votes
Recommended software to open NetCDF files?
Python libraries: xarray and hvplot
This is a rather generic answer for opening and quickly visualizing a netCFD file with python. It is not specific to condensed ...
- 1,655
9
votes
Accepted
Duplicate structure in PDB format?
You can use Packmol to achieve this. Below is an example script
...
- 1,291
8
votes
Can a file in the Gaussian CUBE format be voxelized?
I'm not sure precisely what you mean, but if you want to convert a Cube file to an ($N\times4$) matrix where $N$ is the number of points and the 4 columns are (x,y,z,value), you can try the following ...
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