Questions tagged [software]

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

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Translate INCAR to Python script using ASE

I am considering using ASE to translate my old work into a Python script. I already have the INCAR and POSCAR KPOINTS files. Is it possible to let ASE read these files and generate Python scripts that ...
6
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1answer
61 views

How to predict protonation state of molecules in water?

I'm interested in predicting the protonation and tautomer state of organic molecules (typically CHNOS) at near pH 7 in water. I've used tools like Schrodinger's Epik / LigPrep before, but they ...
4
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0answers
9 views

Is there a dynamic read-out of angles/distances with Jmol?

For up to ten non-hydrogen atoms, MolCalc allows an installation-free optimization of organic molecules, and subsequent computation of e.g., vibrational frequencies in the range of about $40 \dots \pu{...
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0answers
31 views

Run VESTA on Ubuntu 20.04

I tried to run VESTA on Ubuntu 20.04, but the program crashes. I checked all the dependencies listed in the document but didn't figure out the reason. I found someone who also meets the same problem, ...
6
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0answers
36 views

Any Open-Source, Free Software That Can Be Used to Computationally Calculate Binding Affinity Between Two Molecules?

There are programs out there which calculate the binding affinity between a ligand and a target protein (Autodock 4, Autodock Vina, Chimera... etc). Is there any analogous program that can be used to ...
5
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0answers
17 views

Autodock Vina Error on Chimera: Service "local" unavailable

I was confronted with an error, upon trying to dock a minimized ligand to a target protein, that the "service 'local' [is] unavailable". I then realized that one must have an executable file ...
10
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1answer
77 views

Recommendation of open source software that could build Heterostructure models visually?

I am looking for open-source software that could help me to build Heterostructure models visually, I've been working with BIOVIA Materials Studio before, but I got no valid license now, so I'd like to ...
5
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1answer
114 views

Unrecognized or duplicated keyword error using ORCA

I wanted to run ORCA 5.0.2 with the following input: ...
5
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0answers
33 views

Segmentation fault during execution of Orca 4.0.0.1

I would like to use Orca 4.0.0.1 under the following Linux version: ...
7
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2answers
109 views

What software can be used for Crystal Surface Calculations?

I have been unable to find software for making surface calculations, so I currently perform surface calculations in LAMMPS by creating crystal structures in python, before rotating and cutting them ...
20
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10answers
4k views

GUIs for Quantum Chemistry... Where are they?

I have a general and maybe a little silly / funny question. Why don't most CompChem or QuantumChem software have a GUI? SIESTA is trying with Simune as far as I know, but even proprietary software ...
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42 views

Benchmarking Monte Carlo simulations of polymers

I have written a simulation engine in C++ to run a Monte Carlo simulation of polymers on a lattice. My code basically plants a polymer on a lattice, and performs certain Monte Carlo moves, including ...
9
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1answer
190 views

What software can I use for gas adsorption calculations?

We are from a new research group working on matter modelling. Currently our work has focused mainly on classical Molecular Dynamics (MD), Lattice Dynamics (LD) and ab-initio methods. For these, we ...
10
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1answer
95 views

What's the Theory Behind Nudged Elastic Band?

I'm interested in doing some calculations to model the interstitial addition of nitrogen into a structure and I'm thinking of using Nudged Elastic Band to do it. From what I have read you start with ...
7
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1answer
55 views

Frequency error in Gaussian CASSCF(10,10)

I am stuck in calculating the frequencies of one optimised geometry for naphthalene CASSCF(10,10) with Gaussian 16. I have optimised its geometry and checked the active space is the pi system of it, ...
5
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1answer
97 views

Modify ORCA orbitals for CASSCF

I have run a HF calculation on naphthalene and I have checked the MOs that have been obtained. Now, I have to select my active and inactive orbitals for CASCF(10,10). As there are 34 occupied orbitals,...
9
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61 views

How to efficiently adjust the AMIX_MAG and BMIX_MAG parameter in VASP calculations?

I'm trying to calculate the magnetic anisotropy energy of Cr2O3 by comparing the total energy difference of the system in different spin configurations (in-plane and out-of-plane). However, when ...
8
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1answer
65 views

How to use VEDA to analyze vibrational energy distribution?

In my bachelor thesis, I am trying to use the VEDA program to analyze the vibrational energy distribution to associate different vibrations to the calculated modes from gaussian. I am stuck now ...
6
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1answer
44 views

What is the meaning of Coulomb Subtraction?

Specifically, in the General Utility Lattice Program (GULP) 2003 paper, in the methods section on Two-body Short-range Interactions we have the following: For covalently bonded atoms, it is often ...
4
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0answers
28 views

Discrete lattice polymer simulations

I am trying to develop phase coexistence curves for generic polymers. Of course, I can use standard Flory theory free energy functionals to do this, but I want to define my nearest neighbor polymer-...
5
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2answers
329 views

Soil Modelling: Getting accurate Thermal Conductivity values

Context: We perform a lot of CFD (Computational Fluid Dynamics) modelling for our clients (geothermal, construction, general underground engineering, etc) where we have to model temperature flows and ...
4
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0answers
39 views

Simulate drain current gate voltage for QDFET [closed]

I've modeled a QDFET transistor of sorts at an atomic scale, as it's not a standard MOSFET, and was wondering how to do a drain current/gate voltage simulation. I don't really have any idea how to ...
5
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0answers
73 views

How can I add double bonds to Triazine-derivatives for OpenBabel generation of pdbqt files? [closed]

The double bonds are initially present at the sdf file but disappear or are misplaced after .pdbqt conversion. I tried all kinds of combinations using renumbering ...
12
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1answer
294 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 ...
5
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1answer
92 views

How to run multiples VASP files named as POSCAR-XYZ

Is it possible to direct VASP to read a POSCAR-xyz file instead of reading the default POSCAR? For example, I want to run VASP in the Quantum ESPRESSO format: ...
5
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0answers
73 views

How to extract Cartesian gradient with more digits than 8 using Gaussian? [closed]

I would like to obtain the Cartesian gradient from a Gaussian formatted checkpoint file with more digits than 8 (specified in scientific notation). Is there any way to do this?
5
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1answer
53 views

Convert PSP8 pseudopotential files to UPF format

Is there a way to convert psp8 pseudopotential files (used for abinit) to UPF format (used for Quantum ESPRESSO)? I noticed there is the upfconv.x utility in ...
7
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0answers
64 views

How can I calculate the exchange energy for a molecule in PySCF? [closed]

I am trying to generate exchange energy separately in pyscf but didn't see a way to do that. For correlation energy, it's fairly simple but do you have any idea how to calculate exchange energy?
4
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0answers
39 views

Calculating emission spectrum of organic compounds by DFT. Can someone elaborate in terms of calculating it for aggregatrion induced emission? [closed]

I am planning for the calculation of emission spectra of organic compounds showing the phenomenon of aggregation-induced emission (AIE). Can someone help me get started?
9
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2answers
250 views

How do you generate 3D electron density from fchk file without the Gaussian software?

I'm trying to reproduce some results from a paper with fchk output files containing DFT calculations. The paper details how to produce the 3D electron density using Gaussian software, but since I don'...
16
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2answers
419 views

How should I organize and keep track of a huge number of calculations systematically?

Doing matter modeling generates vast amounts of data. We might most probably be working on different projects simultaneously. We definitely will have to revisit old data for revisions, post-processing,...
11
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1answer
298 views

What units are used in Gaussian 16 for dipole derivatives output?

I ran a frequency analysis employing Gaussian 16 on MP2/6-31+G(d,p) level of theory with the keyword iop(7/33=1) in order to have access to dipole derivatives with ...
14
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1answer
561 views

GUI for DFT calculations

I am a beginner in DFT. Can someone suggest a good DFT software with a GUI for simulating dipole moments and optical absorption spectra in an organic crystal? I have tried the Burai GUI of Quantum ...
8
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1answer
82 views

Excited states using ORMAS flag in GAMESS

I am trying to calculate the excited states using single reference CISD on $\ce{CH3OH},$ using ORMAS' CI-X option in GAMESS. As a test example I am using the $\ce{CH3OH}$ that has 2 core, 7 occ. ...
12
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1answer
165 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 ...
7
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2answers
479 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
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1answer
93 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
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1answer
101 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
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1answer
86 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
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1answer
70 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 ...
32
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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 ...
10
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1answer
225 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
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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
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2answers
176 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
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1answer
147 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, ...
8
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0answers
57 views

What could be the possible causes of the energy difference in the following calculation using Octopus (TDDFT) code? [closed]

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. ...
9
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1answer
172 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
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1answer
37 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
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3answers
791 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
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1answer
87 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 ...