Questions tagged [software]

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

Filter by
Sorted by
Tagged with
9
votes
1answer
90 views

Functional group detection from geometry

I am currently looking for an efficient way to detect common functional groups - that is, characterize whether a molecule is an alcohol, an aromatic compound, etc. - in a larger database consisting of ...
6
votes
2answers
48 views

Converting SDF to PDBQT using OpenBabel

I want to convert several molecules from sdf format to pdbqt using OpenBabel. However, I can't find ...
4
votes
1answer
59 views

Excited determinants, electronic partition function and thermochemistry calculation

While studying statistical thermodynamics I came across the partition functions, which connect the quantum world to the macroscopic world. I understand that partition functions are used to calculate ...
9
votes
1answer
79 views

What do the parameters at the top of an FCIDUMP file mean?

A while ago I wrote a simple program that takes in an FCIDUMP file (generated by MOLRPO) and can determine matrix elements (or ...
9
votes
1answer
60 views

What software can do RNA secondary structure prediction?

This question is a follow-up to this previous question. I have learnt there that there are reasonable ways to predict RNA tertiary structure. Here I inquire about how to predict RNA secondary ...
9
votes
1answer
60 views

What software is a software for RNA tertiary structure prediction?

It seems that the prediction of protein folding is a pretty advanced area. Are there options based on some GDT-like measure? For me, it has relevance in connection with the origin of life (cf. RNA ...
30
votes
5answers
2k 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 ...
9
votes
1answer
106 views

How to calculate FCI matrix elements from an FCIDUMP file

I'm interested in writing a simple program (as an exercise) that takes an FCIDUMP file (e.g. from a Molpro calculation) and can determine FCI matrix elements (e.g. to construct the entire FCI matrix ...
21
votes
5answers
4k views

What software will allow me to combine two images?

I have seen in many presentations and publications, things like a human on a molecule (for example). What software can do this? It's for a presentation I'm doing.
10
votes
2answers
116 views

Programs/Libraries for calculating solvent excluded surface and excluded volume

Given the 3D structure of a molecule (e.g. as *.mol) and a probe radius r, I want to calculate the solvent excluded surface (SES)...
10
votes
1answer
67 views

How to determine occupied and closed orbitals for a Molpro CASSCF calculation?

I am currently working with Molpro, to which I am completely new, trying to run some calculations on $\ce{PdO}$. From literature I have gathered that the ground state is given by $^3\Sigma^-$ state, ...
6
votes
0answers
31 views

What could be the possible causes of the energy difference in the following calculating using Octopus (TDDFT) code?

I am trying to do a simple ground state energy calculation of methane molecule using the Octopus (TDDFT) code. The example is already available in the octopus manual. ...
8
votes
1answer
149 views

How are molecular orbitals constructed from the coefficients and basis set?

When an SCF calculation is done in a QM program, the MO coefficients of the solution are printed into the output. Now, graphical softwares can plot 3D molecular orbitals from these coefficients, ...
7
votes
1answer
33 views

The number of long-range interaction pairs in Tinker

I tested MM calculation of a benzene molecule with Tinker. The following is the xyz file used for the input. ...
11
votes
3answers
738 views

How to build a nanocluster?

What are the software tools (if possible open source) or methods we can use for constructing a nanocluster, most preferably with high symmetry such as icosahedron, octahedron, cuboctahedron etc. ?
6
votes
1answer
44 views

Understanding QuantumEspresso Toolbox through Maestro

Anyone here uses Quantum Espresso through Maestro can tell me a bit more about the calculation panel setting: I understand that -npools option must be divisible by ...
7
votes
0answers
291 views

Is there any code for local-orbital ab initio tight binding molecular dynamics other than fireball?

I was searching for a local-orbital ab-initio tight binding implementation of molecular dynamics and Ive found a code called fireball. Ive tried to compile it but the code seems to be buggy and there ...
6
votes
1answer
48 views

Band structure output from Exciting - what are the X units?

I'm using Exciting Code to calculate some electronic band structures. Starting with the example of Si I get sensible output and can plot BAND.OUT and BAND-QP.OUT using PLOT-gwbands.py or directly in ...
6
votes
1answer
53 views

How to calculate Transport coeffiecients for 0 D systems?

I would like to calculate the thermal transport coefficients like Thermal Conductivity, Seebeck coefficient etc for thermoelectric 0 D systems (quantum dots, nanoclusters ..etc). For bulk materials, ...
5
votes
0answers
26 views

Interpreting Critic2 charge analysis in metallic systems

I'm using Critic2 software to perform post-processing of the charge density of metallic alloys. With the charge density obtained from the Self-Consistent-Field calculation (for that I'm using Quantum ...
10
votes
1answer
134 views

Calculating/Visualizing electronic density from orbital information written in the Molden format

I'm trying to obtain an electron density from orbital information written in the Molden format by the formula, $$ \rho(\mathbf{r}) = \sum_{i}^{occ} |\phi_{i}(\mathbf{r})|^{2}. \tag{1} $$ Is there any ...
11
votes
2answers
160 views

Recalculate atom positions to account for periodic boundary conditions

I have the output of a simulation done using Periodic boundary conditions (PBC), however, the atom positions have been resolved, i.e. there are atoms outside the PBC-box now. Is there a software/...
12
votes
0answers
73 views

Recent developments in QM/MM for Molecular Dynamics

I am looking for new QM/MM methodologies which have recently developed and implemented into MD packages. Any applications or molecular systems studies with these methods can be used as an example as ...
13
votes
1answer
232 views

Software for Exact Diagonalization of quantum spin Hamiltonians in 1D and 2D

I'm looking for software (which can also run in parallel) for Exact Diagonalization of Quantum Spin Hamiltonians in 1D and 2D (e.g. Heisenberg Model) consisting of a large number of spin sites. There ...
16
votes
2answers
399 views

What's the best way to compare two DFT codes?

What's the most efficient way to compare the two DFT codes in terms of computation time, basis sets (for example, one plane wave vs one atomic orbitals), functional performance, etc.?
9
votes
0answers
56 views

How to create a Potential Energy Surface in Chemcraft?

The Chemcraft website says that it is possible to create a potential energy surface. Nevertheless, it doesn't work for my Gaussian scan job. ...
11
votes
1answer
100 views

Calculating RMSF in VMD

As a part of my coursework I have to calculate root mean square of fluctuation (RMSF) of a protein trajectory over the last 5 nanoseconds of simulation. I have used the inbuilt ...
8
votes
1answer
215 views

Why do we need to build a supercell to use the DFPT in Phonopy interfaced with VASP?

The following passage about the merits of density-functional perturbation theory (DFPT) is extracted from this seminal paper: Phonons and related crystal properties from density-functional ...
10
votes
1answer
113 views

Generating SOAP descriptors in python

What is the best python package to construct Smooth Overlap of Atomic Positions (SOAP) descriptors given SMILES representation of a molecule? Is this even possible without providing 3D geometry? An ...
9
votes
1answer
70 views

Can you list some useful code snippets for processing quantum ESPRESSO output files?

I know that this is quite general. But we have all written code for processing output files from various dft codes. The functionality of which, may range from analysing time traces to finding ...
18
votes
2answers
375 views

What is a chemputer?

I first saw the term "chemputer" when reading about the work of Neil Ostlund (who you may know as one of the authors of the famous book "Modern Quantum Chemistry"). Based on the ...
10
votes
1answer
112 views

What are the trade-offs setting DIRSCF to either .TRUE. or .FALSE. (the default) in GAMESS (US)?

The first software I used to run calculations was Gaussian09. When submitting a input, I used to see a pattern of resource usage where the allocated CPU quickly maxed out, remaining high most of the ...
6
votes
1answer
59 views

How better is PAW available in VASP when compared to that present in PS Library?

Papers with DFT calculations that use VASP work with PAW pseudopotentials which are also available in PS Library. I assume they are different since VASP is commercial. Given that, how different are ...
7
votes
2answers
966 views

Computer simulation of squeezing flexible objects with force

I am looking for any software, or scientific works, or search phrase in the field of simulating graphic modeling of squeezing objects. I would like to simulate packing very oddly shaped soft elastic ...
5
votes
1answer
29 views

What are some ways to model disequilibrium processes with current software?

Its normally that case that most material modeling techniques rely on energy minimizations, which result in the equilibrium solutions for most chemical of physical processes. While this is great for ...
8
votes
1answer
71 views

What software can perform block analysis on time sequence data?

I have a .xyz file for a trajectory and I want to perform block analysis on it, and to find the decorrelation time and to perform analysis on that as well. What ...
13
votes
0answers
108 views

Empirically determining thermostat damping factor

Is there a way to determine an appropriate thermostat damping factor given a timestep size and a numerical integration method? I am computing a set of simulations in LAMMPS, using ReaxFF, tracking ...
5
votes
0answers
81 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
votes
3answers
548 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
714 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
85 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
165 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
138 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
79 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
65 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
73 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 ...
16
votes
0answers
136 views

What are the tools available for point defects calculations?

As far as I know, there are mainly PyCDT, PyDEF, pylada and some part of pymatgen. As a new user to those tools, which one would be a good choice? It would be appreciated if you could explain one of ...
11
votes
2answers
229 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
147 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.