Questions tagged [open-source]

For questions seeking open source software or databases to solve a modeling problem.

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8
votes
1answer
312 views

Given the adjacency matrix of a molecule, how can I get a graphical representation using only open source software?

In Huckel Method, by numbering the sp2 carbons in a molecule with conjugated double bonds, we can assemble its secular determinant in a form similar to the adjacency matrix of a graph. Taking trans-...
9
votes
1answer
399 views

Why is the planewave codes ecosystem healthier on free/opensource software adoption, when compared to codes supporting atom-centered orbitals?

Regarding the branch of matter modeling that deals with electronic structure methods, I think we can divide it in two camps: Those who work mostly with planewave-based software, geared towards ...
12
votes
1answer
234 views

Comparing GAMESS, OpenMOLCAS and Psi4

Over the years many open-source ab initio packages have been developed and the diversity in subroutines, methods and portability (ability to interface with other software) is quite varied for ...
8
votes
1answer
117 views

What are open source options to simulate kinematical electron diffraction patterns?

I tried using the python package diffsims. I get an image, but not a diffraction pattern I was expecting. ...
12
votes
2answers
127 views

Is there some free software to do Frank-Condon analysis?

I know Gaussian 16 can do it, but are there some free programs that can? For simple excited state calculations using TD-DFT, we can use NWChem and Octopus. Can these do Franck-Condon factors?
31
votes
5answers
3k views

What is a good replacement for Gaussian?

When I started studying computational chemistry (circa 2007), my supervisor used to tell me about the controversy surrounding Gaussian, Inc. regarding the banning of researchers involved in the ...
12
votes
1answer
101 views

Metropolis algorithm reduces energy in molecular simulation, but does not decrease euclidean distance

I am using an open source python package openmmtools to run a simple molecular simulation problem using the metropolis algorithm. I first load a default system of particles (alanine-dipeptide in ...
12
votes
1answer
201 views

How to get more significant digits from OpenBabel?

I am generating conformers from SMILES string using OpenBabel. The shell script looks something like: ...
10
votes
0answers
85 views

Periodic polarizable QM/MM embedding

Are there any standalone open source software codes available for periodic polarizable QM/MM embedding MD simulations? In my knowledge, CP2K only has the option for electrostatic embedding and other ...
16
votes
2answers
888 views

Open Source PyMol Conda Package: UnsatisfiableError

I'm having an issue installing the open-source version of Pymol using Anaconda on Windows. I have Python 3.8.3 installed and when I try to add the package with Conda using ...
9
votes
1answer
607 views

How to do spin polarization calculations using Quantum ESPRESSO?

I am currently new to DFT calculations in Quantum ESPRESSO. Though, I have read some research papers for determining spin polarization and Half-metallicity in certain Heusler alloys. These research ...
10
votes
5answers
2k views

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

I am doing DFT calculations with pw.x executable in Quantum Espresso. For this we have to choose right K-points grid in order to perform error-less calculation. But I have no idea about how can I ...
13
votes
5answers
485 views

DFT software package for a beginner?

I would like to do start doing some basic calculations using DFT. I am interested in solid state physics of strongly correlated materials in 3D (for example high temperature superconductors) or 2D (...
9
votes
3answers
94 views

Which non-commercial softwares can be used to model amorphous carbon?

I have a fair idea of generating and modeling crystalline materials but what non commercial software programs can be used to model amorphous carbon of a specific dimension, say a $6\times6\times6$ Å ...
9
votes
2answers
220 views

How to calculate the nuclear energy derivatives in molecular mechanics?

In molecular mechanics, the energy is often written as a sum of bonds, angles and torsion energies, and an electrostatic term, e.g. $V = \sum_{bonds} K_r (r-r_{eq})^2 +\sum_{angles}K_{\theta}(\theta -\...
9
votes
1answer
182 views

Freely available constrained DFT implementations

What free quantum chemistry packages that have constrained DFT (CDFT) implemented? A google search does not reveal anything, perhaps there may exist a better resource to find the packages.
10
votes
4answers
787 views

Codes for post-processing Gaussian cube files?

I have generated MOs of a molecular system and I need to recreate its electronic density via $\rho(r)=\sum_{A_i}|\psi_i(\mathbf{r})|^2$ where $A$ is a set of occupied MOs. I am trying to do this via ...
14
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8answers
2k views

What are some free programs to do docking?

I'm interested in doing molecular docking. What are some free programs for it and what are their pros and cons?
17
votes
2answers
2k views

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

The adoption of atom-typing allowed for the creation of incredibly widely used force-fields (FF) such as GROMOS/AMBER/OPLS and many more. Because of the assumptions ...
27
votes
9answers
4k views

Which Linux distribution is best for Matter Modeling?

In some science fields there are efforts to provide customized distributions, so you can get a productive environment with minimum set-up overhead. For example, in high energy particle physics, we ...
21
votes
3answers
3k views

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?

The codes for quantum mechanical calculations make heavy use of linear algebra, and it seems most of them delegate this task to time-tested and highly optimized libraries, instead of trying to deploy ...
15
votes
4answers
262 views

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

What is a good open source software for calculating the rotational and translational entropy of molecules? The National Institute of Standards and Technology does not provide standard molar entropy ...
16
votes
1answer
113 views

What are typical RPA capabilities of plane-wave codes?

Plenty of standard plane-wave codes are able to compute correlation energies on top of DFT solutions using the random-phase approximation (RPA). I was wondering what the typical capabilities are in ...
12
votes
3answers
184 views

Is there a repository for DFT pre/postprocessing scripts?

While DFT calculations are a key step in a simulation workflow, generally more steps are required to obtain a meaningful result. This can include pre/post-processing of results to e.g. compute ...
14
votes
3answers
272 views

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

I am very interested in doing transport calculation with SIESTA. My problem is that it is a little hard for me to understand and setup the input files to be used with TranSIESTA (the module that do ...
16
votes
1answer
76 views

Protein cavities - methodological starting point for basic characterization

Characterizing surface properties is important for understanding how proteins execute their function by interacting with other molecules. This includes characterizing cavities. Perhaps the simplest ...
18
votes
2answers
362 views

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

I tried to recover a .CIF file (Crystallographic Information File) with the crystal structure for the compound discussed in a paper by Reuter et. al.[1], strontium hydroxide octahydrate - $\ce{Sr(OH)2·...
21
votes
2answers
148 views

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

Several years ago, I became familiar with nanoHUB for accessing open-source codes and software specifically for computational materials science at the nano-scale as well as PFHub that gives you access ...
18
votes
1answer
113 views

What are some servers that are able to host and share our research data?

Now a days, due to some publish-or-perish politics that gives place to many cases of plagiarism and fake data/results, some journals are asking to submit (and share) the data used in the research. In ...