There isn't a silver bullet for this, so in my humble opinion there isn't a "best" Linux distribution for this. Just as Kali is not "the best" for security and Scientific Linux is also not advertised as the "best" for HEP. They are just good enough alternatives that tackle some issues that may seem helpful for many users, such as including many things and ...
Official website: https://orcaforum.kofo.mpg.de/app.php/portal
What is ORCA?
ORCA is a general-purpose quantum chemistry program package that features virtually all modern electronic structure methods (density functional theory, many-body perturbation, and coupled-cluster theories, and multireference and semiempirical methods). It is a flexible, ...
MOLCAS is now in it's 5th decade! The first version was written in the 1980s by the group of Bjorn Roos, one of history's giants in quantum chemistry. It can do many of the things most mainstream quantum chemistry packages can do: integrals, Hartree-Fock, DFT, MP2, coupled cluster, geometry optimization, etc., and while it can do "single-...
For your workstation or laptop the best linux distribution is Ubuntu. Many of the recommendations here, like CentOS, are great for servers, but you might also have a laptop or desktop computer that you use for developing your code and running simulations. Ubuntu has gone much further than other linux distributions in developing a consumer-grade user ...
Susi Lehtola's answer makes some good points, and I will elaborate on two of them:
The Linux distributions mentioned in your question, which cater to specific communities (e.g. Scientific Linux for particle physics, MathLibre for math, Kali Linux for cybersecurity) are descendants of much more widely-known distributions, so they are not acutely ...
First, there are general-use repositories that are not specific to materials modeling.
Zenodo. Like several other approaches, each project gets a permanent DOI associated with it, and new versions can be uploaded with the same unique parent DOI for the project and version-specific DOI. One major upside of Zenodo is that it is managed by CERN, which is ...
OpenBLAS is a free, open-source BLAS library that has fast support for even recent processors. (It is based on the earlier, famous GotoBLAS library which became obsolete years ago.) OpenBLAS is also multi-platform: in addition to x86 and x86_64 it also supports other architectures like ARM and PowerPC. OpenBLAS also has runtime CPU detection; if you compile ...
You can use the free software VESTA for creating a new structure by following steps
From the file menu choose New structure
Go to Unit cell panel and choose the space group of the structure
Enter the lattice parameters in the same panel
Change to Structure parameters panel and enter x,y,z and Ueq of each atom one by one
Save the structure and after ...
Scientific Linux is a rebuild of Red Hat Enterprise Linux. It started out before the CentOS project really took off. Nowadays CentOS is officially supported by Red Hat, but Scientific Linux still exists on its own.
Since both CentOS and Scientific Linux are just rebuilds of RHEL, all three should be binary compatible, and you should be able to use the same ...
Psi4 is a fully open-source quantum chemistry package that is gaining a lot of interest in my community (computational) combustion chemistry.
Here is the manual for the latest release: it has most, if not all, of the theoretical methods (HF, DFT, CC,...) and also lots of interfaces and integrates into C++ and Python (sadly no Fortran).
The bonus on it ...
(to simulate continuous material)
CAELinux's official page states:
Based on the open-source CAD/CAM software such as Freecad, LibreCAD, PyCAM and Slic3r and CAE softwares like Salomé, Code_Aster, Code_Saturne, Calculix, OpenFOAM and Elmer , you can design your CAD geometry, perform multiphysics simulations to optimize your design, generate G-code ...
For many researchers, GAMESS is the "natural" substitute for GAUSSIAN. Developed and maintained by the group of prof. Gordon (also a banned GAUSSIAN user, see image below).
Official website: https://www.msg.chem.iastate.edu/gamess/index.html
What is GAMESS:
GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can ...
ForceBalance is one approach which aims at making it easier to create force fields from a combination of theoretical and experimental data. I believe it's within the OpenMM framework.
The paper on the work can be found here
From the GitHub page it says
"The purpose of ForceBalance is to create ...
Quantum Mobile Virtual Machine
Disclaimer: Not exactly a Linux Distibution but a Virtual Machine (VM)
Quantum Mobile is a virtual machine for computational materials science.The VM is based on Ubuntu 18.04.4 LTS with VirtualBox 6.1.4.
It comes with simulation codes - BigDFT, cp2k, fleur, Quantum ESPRESSO, Siesta, Wannier90, yambo, together with AiiDA and the ...
There are numerous free tools that can do this with command-line based calls to the underlying codes, from the venerable 'make' to more modern alternatives like 'DoIt' and 'snakemake'. A lot of these 'workflow systems' seem to be used in the bioinformatics community.
For a visually-edited 'blocks and wires' approach, perhaps KNIME (assuming a free version is ...
They do not have an easy interface, however, there are some tutorials and examples that can be used, you can use as an input parameter: github.com/siesta-project/tutorials.
The input file is in .fdf, you can try to generate only the structure through nanolab> 2015 with commercial or academic version.
But the calculator will always be set manually, with ...
This is not the exact response to your question, but I would like to present a very good youtube channel QuantumNerd. Its content is vast and interesting, concerning materials simulation. Recently, he posted a video about a project of making multi-platform GUI for Quantum ESPRESSO, he mentioned though the possibility of growing the project to other DFT ...
As a historic note, I found an example of a effort in this direction, in the past. A modified KNOPPIX targeted at molecular modeling with Gamess-US. It was called the VigyaanCD. Unfortunately it appears to be a defunct project by now. It was released in 2005 and I could not find any updates since then. The Gamess site has the following description:...
The identification of cavities, for drug design, is beyond the geometric characterization (aka volume).
The server and individual software, beside the geometrical cavity determination, characterize them following their functionality and extent of solvent exposure, what sites are suitable for occupancy by hydrophobic groups or by ligand hydrogen-bond donors,...
As I understand, OP's requirements are
Do basic calculations using DFT
Prefer open source software which is easy to use
Interested in DFT only as a tool to calculate properties of materials
Not interested in learning details of DFT/software developing
Since the OP is already aware of Quantum ESPRESSO and is interested only in calculating basic ...
Any quantum chemical program should calculate these for you as part of a vibrational calculation. Generally, the vibrational, rotational, and translational entropies will be given.
The critical task is to start with an optimized geometry with a good method - and ideally some level of conformer search (i.e., to make sure you have a low-energy conformer).
CDOCKER is docking program developed by the Brooks Lab and it works with CHARMM. CHARMM does have a free version named charmm. The difference is no DOMDEC or GPU high performance modules.
Pros: Rigid and flexible receptors, highly customizable
Cons: Need to get free charmm, creating scripts can sometimes be laborious, no high performance GPU modules
As already specified in the previous answers, the choice of K-Grid mesh should be taken upon verifying the convergence of the desired quantity. We usually start with the convergence of the total energy, but for other properties like optical spectra, for example, the converged grid with respect to the energy should not be enough, and a denser grid is usually ...
The PDB file format has a strict specification on the number of columns, etc. (Consider that some proteins have very large sizes, so distances can be many Ångstroms.)
Thus, the number of decimal places are generally given by the file format.
Some people have asked why Open Babel doesn't give more decimal places, e.g., in the XYZ format, which is, in ...
Psi4 and NWChem
For open source software to perform this task, I can think of Psi4. It's probably the easiest to download/install and get going. It has the usual computational chemistry methods along with ab-initio/SAPT methods.
Some details can be found here:
psi4 thermochemistry: http://www.psicode.org/psi4manual/master/...
The NIST Materials Resource Registry is not limited to computational resources, but refers to many of the codes you're looking for. Searching for "hub" only turns up two listings, both of which are tied to nanoHUB and Purdue.
Like many other parameters in QE one of the best methods is to simply test yourself and weight your options.
You may start with 1x1x1 and go to 3x3x3 for example and check the following.
Do you get convergence?
What is final energy?
What is dE in the final step?
(plot the above parameters to see the diminishing returns)
Then determine computation time ...
If you're using Linux its better if you install such packages using the apt-get method.
apt-get install pymol
I've encountered a similar error while installing MatPlotLib through conda.
For more info you can follow this link:
Hope this helps :)
I was able to find a workaround to get open source PyMol installed on Windows. Christoph Gohlke at the University of California has a large library of precompiled Python wheel files of various scientific packages, including PyMol. I was able to find a Windows version for Python 3.8 pymol‑2.5.0a0‑cp38‑cp38‑win_amd64.whl and after downloading this file, I was ...