Questions tagged [software]

For questions about matter modeling software. Questions can be about usage or recommendations.

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6
votes
0answers
105 views

Fix deposit and USER-REAXC: pre-allocating memory for atoms when using LAMMPS with ReaxFF

I would like to use "fix deposit" with ReaxFF to add atoms to a simulation in which I deposit molecules on a surface. I have built working scripts for my system with other force fields. ...
13
votes
5answers
2k views

Can I use two different codes?

Can I use one code for geometry optimization and another code for a single point calculation on that optimized geometry? Can one publish results like that?
11
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4answers
890 views

How to make the input generator plugin work in Avogadro 2 on GNU/Linux?

It seems Avogadro was phased out in Ubuntu 20.04 (Focal Fossa) and derivatives like Mint 20 (Ulyana). Now the version available in the repositories is Avogadro 2. If you had Avogadro installed in 18....
7
votes
2answers
1k views

Why the Open Babel submenu is faded out in Avogadro 2 and I can't optimize geometry in Mint 20?

It seems Avogadro was phased out in Ubuntu 20.04 (Focal Fossa) and derivatives like Mint 20 (Ulyana). Now the version available in the repositories is Avogadro 2. If you had Avogadro installed in 18....
9
votes
3answers
93 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 ...
12
votes
1answer
202 views

Is there a software that can calculate collision cross-sections involving molecules with several atoms?

What software currently can be accessibly used to calculate collision cross section using the geometries obtained from DFT? In my case, Q-Chem is used for geometry optimization. The goal is to compute ...
9
votes
2answers
149 views

How to build a simulation model for a molecular dynamics simulation

I have got aggregate of 4 non-protein compounds I would submit for molecular dynamics simulation. The problem is I can't find software capable to do that. Amber, GROMACS, LAMMPS, all of them require ...
7
votes
0answers
95 views

Collective variable to determine the number of bonds in the shortest Hydrogen bond wire [closed]

I am trying to program a collective variable in PLUMED which is basically the number of bonds in the shortest Hydrogen bond wire in a system of water molecules. I plan to use the HBond_Matrix from ...
9
votes
1answer
72 views

Docking proteins with glycans

Do you know of a good software or web server tool that helps doing docking of proteins with rather large glycans? An example I'm interested in is tens of dimers of sugars (or similar), docked to ...
9
votes
0answers
85 views

Is there any code that runs WHAM starting from histograms rather than time series?

I'm looking for a way to run the Weighted Histogram Analsys Method, but I don't have a time series to feed to the code as usually happens, but rather I have histograms coming from the debiasing of a ...
11
votes
2answers
281 views

Moving from VASP to CASTEP for bulk crystal and surface calculations

Can someone that works with CASTEP and VASP explain to me how a workflow might change between the two programs? I am very familiar with VASP but have not used CASTEP before. As an example, assuming ...
9
votes
1answer
179 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.
7
votes
1answer
664 views

Atom legend in VESTA

Is it possible to to display the atom legend in VESTA and export the structure including the legend as a vector/raster image? I found this discussion from 2013 requesting this feature. Has it been ...
8
votes
1answer
142 views

Is this G16 molecular hyperpolarizability error reproducible in other software?

I was trying to calculate the hyperpolarizability $\beta$ of a cluster of two water molecules in Gaussian16 using the route card: ...
10
votes
1answer
124 views

What resources are available to learn how to do something in VASP?

Apart from what is obvious (from a Google Search), what are the various resources available if I want to learn how to do something in VASP (for example, starting an HSE06 calculation)?
11
votes
1answer
307 views

Simulated low energy electron diffraction (LEED) patterns

What modern software supports the generation of LEED patterns? It seems most LEED simulation packages are quite old and do not work on modern hardware. Is there something that prevents common ...
14
votes
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?
6
votes
1answer
53 views

Create an image from scratch with the vectors that represent the Berry phase for parallel transport (classic system)

I want to represent parallel transport as in the following figure, but next to this figure I would like to place a diagram with the two arrows (of the initial state and of the final state that are ...
8
votes
1answer
77 views

Which software programs can be used to study SRR (split ring resonator) based meta-material and its cloaking properties

I have been studying about metamaterials and their amazing abilities to interact with EM Waves. I came across a concept called Metamaterial cloaking (something like Harry Potter's invisible cloak ...
13
votes
4answers
316 views

Is python sufficient for serious tensor network or DMRG calculations?

There are enough tensor-network/DMRG packages that support python (ALPS, OpenMPS, pyUni10) that it would seem (to an outsider) that it's possible to do some substantial work with DMRG without messing ...
7
votes
1answer
58 views

Which non-commercial software can be used to dock two proteins?

I need to dock 2 proteins involved in SARS-CoV-2. They are the spike glycoprotein & membrane protein. I need them to be docked as described in the image below. Since there are many docking ...
11
votes
0answers
113 views

Setting multiple new atype/dtype/itype with LAMMPS fix bond/create [closed]

When creating a new bond in a LAMMPS simulation with the command fix/bond create it is likely new angles/dihedrals/impropers be need to be set. This can be done with the atype/dtype/itype arguments ...
5
votes
2answers
76 views

For software that does not support FCIDUMP format, what format is used and how can we get the software to interact with FCIDUMP integrals?

Complementary to this question: How do the various programs read or write integrals in FCIDUMP format? which attempts to list all electronic structure packages that support the ...
11
votes
1answer
474 views

What does the Neighbor command do in LAMMPS?

I frequently see LAMMPS codes, and almost all of them have the neighbor 0.5 bin command. I completely studied the LAMMPS manual for the neighbour command and did ...
5
votes
1answer
91 views

Why am I losing bonds when I use PACKMOL on two proteins?

I recently started using PACKMOL to pack a few proteins together. I wrote this PACKMOL code: ...
8
votes
1answer
145 views

How do the various programs read or write integrals in FCIDUMP format?

The FCIDUMP format was created by Peter Knowles and Nick Handy circa 1989 and now allows many electronic structure software packages to interact with each other. ...
15
votes
3answers
351 views

What are some codes available for Dynamical Mean Field Theory (DMFT)?

One particularly field of matter modeling is that of strongly correlated materials, heavy-fermion compounds with partially filled 4f or 5f orbitals. In brief, these are materials whose complex ...
6
votes
1answer
57 views

Are there properties that can only be calculated with a given set-up?

If you do a bibliography search about the codes used in matter modeling, you will find a large list. I played with a few of them (both free and commercial) and one of my findings is that the ...
11
votes
6answers
1k views

How do I extract a molecular structure from a CIF file?

When I open a CIF file of a crystal structure in a typical molecular editor like Avogadro, then I just see a few symmetry-unique atoms scattered around the unit cell. But I don't see the full molecule ...
10
votes
1answer
181 views

How to interpret molden AO/MO coefficients?

A simple calculation with Molpro 2012 on H2 molecule in cc-pvtz basis produces a molden file with 28 molecular orbitals. Each MO is defined with 30 AO/MO coefficient, but the number of symmetric AOs ...
11
votes
1answer
185 views

Dealing with symmetry of ordered primitive cell during DFT structure relaxation

I have a large disordered cubic structure that I would like to do AIMD on to look at cation diffusion. I found the primitive cell and then ordered it to create several configurations. I will then ...
9
votes
0answers
287 views

I wrote a Python code to do MD for a Lennard-Jones fluid but the VACF is wrong: What might be the problem? [closed]

I am trying to write a molecular dynamics simulation for a Lennard-Jones fluid in a box with periodic boundary conditions. The box has no net momentum. I am writing this in python. I have written a ...
14
votes
1answer
221 views

Great computer graphics for matter modelling

I am trying to write some code to automatically generate a judicious set of graphics from DFT/fn-DMC calculations so that users can sanity check their results quickly. My literature review has found ...
13
votes
4answers
306 views

What are some open-source all-electron DFT alternatives to Wien2K?

Since the beginning of the century, Wien2K has proven to be a very powerful player in computational condensed matter and materials physics. Wien2K is an all-electron periodic DFT code based on the ...
13
votes
1answer
161 views

What is the speed/time required for DFT simulations?

I am currently designing a toy model to calculate an interatomic potential (for an infinite repeating lattice) this toy model needs to scale and perform better than DFT simulations. But sadly I have ...
16
votes
1answer
409 views

How to map the electrostatic potential from GAUSSIAN, on a solvent accessible surface?

Gaussian cubegen and surface generators in Gaussview seem to only allow to map the ESP on SCF densities. I used G16 for the ESP generation. I would like to plot it on the solvent accessible surface. ...
11
votes
0answers
336 views

How to convert a molecular structure made in Avogadro to a LAMMPS coordinate file? [closed]

I was trying to convert a crystal structure into a LAMMPS data file in Avogadro but whenever I type .lmpdat as an extension, it says "The file name is not valid". Can you tell me any ...
14
votes
2answers
777 views

What is the most user friendly software for frequency visualization rendering?

I perform my calculations in Q-Chem and would like to make short movies of IR modes. As of now, I render them with IQmol, but I believe graphics properties (colors and resolution) can be much better. ...
70
votes
6answers
9k views

Did the 2019 discovery of O(N log(N)) multiplication have a practical outcome?

Some time ago I've read this news article, Mathematicians Discover the Perfect Way to Multiply, reporting a discovery published in 2019, where Harvey and Hoeven[1] found a algorithm able to execute ...
16
votes
4answers
477 views

Is there a set of updated, comprehensive benchmarks for speed comparison between different quantum chemistry packages?

I've found a page dedicated to quantum chemistry packages benchmarks, on GitHub, qmspeedtest. But most results there are several years old, and so probably outdated. Is there some place where we can ...
14
votes
1answer
185 views

Software to draw 3d micelle configuration

I am looking for a free software able to draw 3d micelle configuration like the figure attached. Any suggestion?
11
votes
5answers
676 views

Plotting of natural bond orbitals (NBOs)

Which quantum chemistry programs can compute natural bond orbitals (NBOs)? Which visualisation tools can I use subsequently to plot pictures of the NBOs?
17
votes
1answer
90 views

Converging the potential of a dilute binary alloy system using the Coherent Potential Approximation. What troubleshooting options could I take?

I'm trying to converge a dilute fcc alloy consisting of Cu and U, with the Uranium concentration at 0.01% and the lattice parameter of Cu, using Hubert Ebert's Spin Polarized Relativistic Korringa-...
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
5answers
2k views

What software is available to do molecular dynamics on Windows?

Is there a Windows-based molecular dynamics simulation software which is easy to use?
10
votes
1answer
143 views

MM-GBSA from Induced Fit Docking on Maestro

How can an MM-GBSA(molecular mechanics energies combined with generalized Born and surface area continuum solvation) calculation be done from an induced fit docking (IFD) output? I performed an IFD ...
17
votes
2answers
3k views

Calculating HSE06 band structures on Quantum ESPRESSO

I am currently trying to figure out how to compute band structures for my system, using the hybrid functional HSE06. I'm doing this on Quantum Espresso. As I understand, there are a handful of ways to ...
14
votes
3answers
558 views

Is the DYNAMO code developed by LAMMPS still available?

In 2013 it was stated that v8.8 of DYNAMO was the version mostly used for the last 10-12 years. However I am struggling to find the code repository. It was developed by the LAMMPS developers and is ...
14
votes
1answer
89 views

What is the precise location of the grid points/voxels in a Gaussian .cube file?

Assume that we have a cube file that contains Ni * Nj * Nk points, and an origin at 0, 0, 0, where are the data points actually ...
10
votes
1answer
73 views

Can you model Radiation Chemistry with existing MD software?

I'm wondering if it is possible to simulate the chemical changes materials undergo when exposed to ionizing radiation for a finite period of time with Molecular Dynamics (MD) software. In principal ...