31 votes

Which Linux distribution is best for Matter Modeling?

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 ...
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  • 889
24 votes

What is a good replacement for Gaussian?

ORCA 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 ...
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24 votes

What is a good replacement for Gaussian?

OpenMOLCAS 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 ...
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19 votes

Which Linux distribution is best for Matter Modeling?

Ubuntu 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 ...
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18 votes
Accepted

Which Linux distribution is best for Matter Modeling?

Fedora 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 ...
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18 votes
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What are some servers that are able to host and share our research data?

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 ...
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  • 6,852
17 votes
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Since MKL is not optimized for AMD hardware, should I use a math library specific to AMD, or would an open-source one be just as good?

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 ...
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17 votes
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How can I create a .CIF file from x-ray diffraction data in a paper, for compound not found in crystallographic database

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 ...
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  • 8,362
17 votes

What is a good replacement for Gaussian?

Psi4 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 ...
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16 votes
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What is the cutting edge for open-source Force-Field generation?

ForceBalance 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 ...
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  • 7,744
16 votes

Which Linux distribution is best for Matter Modeling?

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 ...
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  • 14.2k
16 votes

What is a good replacement for Gaussian?

GAMESS 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 ...
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15 votes

Which Linux distribution is best for Matter Modeling?

CAELinux (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, ...
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14 votes

Which Linux distribution is best for Matter Modeling?

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 ...
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  • 8,362
14 votes

Is there a repository for DFT pre/postprocessing scripts?

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 '...
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  • 361
14 votes

Is there a (free) GUI to setup transport calculations using SIESTA?

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,...
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13 votes

Are there any open source software for calculating the rotational and translational entropy of molecules?

ASE: Thermochemistry module The thermochemistry module of ASE is able to calculate these for you.
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13 votes

Is there a (free) GUI to setup transport calculations using SIESTA?

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 ...
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12 votes

DFT software package for a beginner?

QuantumVITAS 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 ...
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  • 8,362
11 votes

Which Linux distribution is best for Matter Modeling?

VigyaanCD 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. ...
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  • 3,696
11 votes

Protein cavities - methodological starting point for basic characterization

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 ...
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11 votes

How to know optimal K-points grid values for good DFT calculation?

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 ...
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11 votes
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How to know optimal K-points grid values for good DFT calculation?

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 ...
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10 votes

Are there any open source software for calculating the rotational and translational entropy of molecules?

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 ...
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10 votes

What is the cutting edge for open-source Force-Field generation?

ForceBalance Cody is right, ForceBalance is designed for the task of generating custom force fields. Force fields have a lot of variability in their functional forms, representation of parameters (as ...
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10 votes

What are some free programs to do docking?

CDOCKER 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:...
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10 votes
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How to get more significant digits from OpenBabel?

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 ...
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9 votes

Are there any open source software for calculating the rotational and translational entropy of molecules?

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 ...
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  • 1,227
9 votes

Is there any complete list of open source hubs specifically designed for materials modeling and computational materials science?

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 ...
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  • 291
9 votes

Open Source PyMol Conda Package: UnsatisfiableError

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 ...
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