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For questions about matter modeling software.

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How to fill in all atoms in unit cell starting from a CIF file?

I am trying to write code that builds a unit cell with all atoms explicitly specified, starting from a CIF file of a molecular crystal. The CIF files come from CSD. My first try was to use Gemmi to ...
Alex I's user avatar
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1 vote
0 answers
15 views

(AMBER) Questioning how mask works in MMPBSA

Note: this question was also posted on the AMBER mailing list, but I reposted this question here because I needed answers for this question quickly. Sorry if this is violating any rules... Dear AMBER ...
Leo's user avatar
  • 67
3 votes
0 answers
26 views

martinize issue

PS C:\Users\MALINE\Desktop\martini> python martinize.py -f polypropylene.pdb -o output.pdb ...
068 MALINE M's user avatar
5 votes
1 answer
153 views

Is there a tool for generating nanotube from an arbitrary 2D structure?

I'm working on creating a specific nanotube structure with a non-hexagonal surface lattice. I have the 2D structure of the walls (basically a 3-atom-width structure, alike, but not, a layer of MoS2) ...
Neinstein's user avatar
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1 vote
0 answers
45 views

AMBER fails to generate parameters

I'm new to computational chemistry, and I'm trying to model the enzyme EGFR and a molecule named lapatinib with AMBER. I got a .pdb file of Lapatinib attached to EGFR, and a .sdf file of lapatinib ...
Leo's user avatar
  • 67
3 votes
0 answers
43 views

Adding a molecule in AMBER

I'm new to computational chemistry. I want to model the enzyme EGFR and a small molecule Lapatinib. I got a .pdb file of EGFR at the Alphafold website, and got a .sdf file of Lapatinib at the pdb site....
Leo's user avatar
  • 67
4 votes
0 answers
43 views

What software is fit for calculating an atomic and electronic structure of a newly formed nanocluster after injecting impurities into an initial one?

Let's suppose there is a nanocluster and its structrure is known. The problem is to inject impurities into this nanocluster. The impurities can be injected in different quantitites but consist only of ...
SFriendly's user avatar
  • 1,007
2 votes
1 answer
47 views

How to draw the double perovskite Sr2FeMoO6 by software/hand?

https://tgc.ac.in/pdf/study-material/chemistry/Ionic_Bonding_Sem_II_G.E._and_D.S.C..pdf "In the structure of the double perovskite Sr2FeMoO6, MO6 (M = Fe2+, Mo6+) octahedra share all their ...
Coo's user avatar
  • 131
4 votes
1 answer
69 views

How to use rigid scan with dummy atoms in gaussian?

I am trying to use rigid scan using gaussian 09. In my case, there are three water molecules and I have placed a dummy atom at the centroid of the three water molecules. For simplicity, I want to ...
Pro's user avatar
  • 1,056
4 votes
0 answers
37 views

Rich editing of ASE images

I want to produce some images related to graphene-like materials. I was able to draw them using ASE visualize module after constructing the atomistic model. However ...
Emu's user avatar
  • 41
3 votes
0 answers
50 views

Electronic density of states from not the usual VASP outputs

In a very frustrating development, my VASP has decided to hang at the writing of outputs stage. While I troubleshoot that separately, for the moment I need to get an electronic density of states from ...
Andrey Poletayev's user avatar
12 votes
1 answer
122 views

Software recommendation for drawing these atomic structures?

Anyone familiar what kind of software is used for drawing the atomic strucutres shown in the attached figure?
Jaafar Mehrez's user avatar
5 votes
1 answer
111 views

How are z-matrices represented in the various matter modeling packages?

Is there a standardized format that is commonly used across molecular simulation (or QM) software packages to store z-matrix information about a molecule? For instance, in CHARMM, which is a Molecular ...
Hemanth Haridas's user avatar
1 vote
0 answers
56 views

Free Cloud Computing for VASP Simulation

I am looking for suggestions for a free cloud-computing platform for running the VASP simulations. I do have the VASP license. I am also ok, if I am allowed to use for a week or so. I can also install ...
Schrodinger's user avatar
6 votes
1 answer
188 views

Is there a dictionary for VASP tags to know what they stand for?

I find the short form of the vasp tag are hard to remember. Is there a dictionary what these short form are stand for. For example USA stand for ...
an offer can't refuse's user avatar
2 votes
1 answer
62 views

How to call VASP input files from parent directory

Let's suppose I want to run the same calculation but for different configurations (= different POSCAR). For all calculations I have the same INCAR, POTCAR and KPOINTS. Those could be stored in a ...
Lukas's user avatar
  • 303
7 votes
1 answer
429 views

Why use PySCF/OpenMolcas instead of VASP/QuantumESPRESSO

While I am aware that VASP and QE are widely used for solid-state materials and PySCF/OpenMolcas are primarily designed for molecular systems. I want to know why should I use PySCF/OpenMolcas for ...
Jaafar Mehrez's user avatar
4 votes
0 answers
72 views

Solvation_analysis subpackage for MDAnalysis multi-atom solute

I have a simulation trajectory from DFTB+ for 1 NaNO3 in 32 H2O molecules. The trajectory is in xyz format and I converted a frame of xyz to pdb using openbabel to serve as topology input. I am ...
bhopshang's user avatar
  • 233
4 votes
0 answers
37 views

Which one of the following showing the correct structure Jsmol or Vesta? Or they are just same

Let me explain. I found that the structure for TiFeSi given in the ICSD database using Jsmol software is a little different from what can be obtained using Vesta software using the same cif file ...
Nilabja Kanti Sarkar's user avatar
2 votes
0 answers
26 views

Are there any good tutorials on SHARC-Gaussian interface?

I am an aspiring quantum chemist planning on trying out the SHARC approach to study excited state proton transfer dynamics of organic molecules. I am comfortable with Gaussian 16 as that is the ...
Uranium238's user avatar
4 votes
1 answer
171 views

How to make Pd(111) supercell (√3×√3)R30 via VESTA

How to make Pd(111) super-cell (√3×√3)R30 via VESTA or Avogadro software?
Rubi Agrawal's user avatar
5 votes
0 answers
198 views

How do I install Quantum ESPRESSO on Windows 10? [closed]

Cross posted on LinkedIn Struggling to install Quantum Espresso on Windows 10 for vital DFT calculations due to missing GitHub libraries. Seeking assistance from the LinkedIn community. If you have ...
86_ Kamran Elyas's user avatar
-4 votes
1 answer
103 views

Are these simulator, visualizer, or force field? [closed]

I see that some "names" are available online in relation to MD simulation. VMD NAMD LAMMPS OpenMM GROMACS Amber CHARMM Are these "names" simulators, visualizers, force fields, or ...
user366312's user avatar
  • 2,556
6 votes
3 answers
1k views

Which MD software is preferable for protein simulation?

I see that some free MD simulation software are available online. VMD NAMD LAMMPS OpenMM GROMACS Amber CHARMM Which one above is the most appropriate for protein simulation?
user366312's user avatar
  • 2,556
9 votes
1 answer
3k views

Software for quantum electrodynamics?

I've been reading some beginner books about quantum electrodynamics / quantum field theory (e.g. Feynman's QED book), and basically everything is done at the paper and pencil level. I'm curious if ...
Alex I's user avatar
  • 1,090
3 votes
1 answer
277 views

Transform Supercell to Unitcell

I’ve supercells of around 10,000 Metal–organic frameworks (MOF) structures in CIF format. I’m looking to convert them to unit cells. But I’m not able to find packages (or any other libraries like ...
hari's user avatar
  • 83
8 votes
1 answer
417 views

How may I install the latest version of a software?

This is a follow-up of my previous question here: How to address 'saveGraphic: Method not found' error in automating the generation of figures in avogadro using Python?, at which I was told to ...
Aimun Jawed's user avatar
6 votes
2 answers
131 views

Is there any Python library for returning the atoms of a periodic material within a cube?

Is there any Python package that allows to cut defined by the points (0, 0, 0) and (x, y, z)? That is, it should return all the atoms of the unit cell and periodic images inside the shaded region. (...
ado sar's user avatar
  • 211
5 votes
0 answers
154 views

Actual calculation of Coulomb energy in DFT softwares

I have a question about the actual calculation of classical Coulomb interaction term in density functional theory (DFT) softwares. Of course I understand the form Coulomb energy as: $\int\int \frac{\...
neco's user avatar
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1 vote
0 answers
90 views

Is there a correct way for compiling and installing NWChem software with all modules from a source code on Linux Mint?

I have been trying to compile and install NWChem v6.8 from a source code on Linux Mint 21.2. According to instructions received from chatGPT, the following steps have to be done: Install necessary ...
SFriendly's user avatar
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5 votes
1 answer
187 views

Calculating theoretical density from .cif files

I'm studying structure-property relations in MOFs and have a pool of hypothetical structures in .cif format generated using ToBaCCo code. I want to filter them based on theoretical density, but the &...
hari's user avatar
  • 83
1 vote
0 answers
54 views

Resource recommendation for learning matter modeling for a novice [closed]

I am a starting researcher in condensed matter physics. Hence, i have all the necessary background regarding quantum physics, and condensed matter physics. But what i want to do is to learn different ...
kal92's user avatar
  • 11
4 votes
1 answer
62 views

Software for storing information of large number of atomic structures into database file

Say I have a MD trajectory that contains a million snapshots (i.e. a million atomic structures). Each snapshot contains some calculated information (either by DFT or some force field) such as energy, ...
Shaun Han's user avatar
  • 1,960
4 votes
0 answers
47 views

Why, if the potential is different from the Coulomb one, but has spherical symmetry, the eigenvalues of the system are non-degenerate? [closed]

Question duplicated from here https://mathematica.stackexchange.com/questions/287433/why-if-the-potential-is-different-from-the-coulomb-one-but-has-spherical-symme and here https://physics....
Mam Mam's user avatar
  • 253
3 votes
1 answer
46 views

Creating a beta cristobalite with 200 or fewer atoms

Can someone suggest me a method to generate a beta cristobalite structure with atoms less than 200.? I tried VMD's inorganic builder tool but so far unsuccessful.
Xdrake's user avatar
  • 541
5 votes
1 answer
175 views

LAMMPS error "Two fix ave commands using same compute chunk/atom command in incompatible ways"

I am very new to using LAMMPS. I am trying to obtain some simulations. I was using an older code which had ave/spatial fix style. In the new LAMMPS version it doesn't work so I am switching to ave/...
Gaurav Maurya's user avatar
6 votes
2 answers
559 views

What are some pros/cons of Quantum ESPRESSO and FLEUR?

I want to know the pros/cons of plane wave (PW) pseudopotential (PP) based DFT codes and all-electron full-potential linearised augmented-plane wave (FLAPW) DFT codes. In the title, I mentioned ...
Abdul Muhaymin -Free Palestine's user avatar
3 votes
0 answers
60 views

How to generate pole figures from limited amounts of area detector X-ray diffraction from thin films (explain it like I'm five years old)

Historically powder X-ray diffraction was the go-to method for reconstructing crystal structure. X-ray sources were limited in intensity and emittance and so to collect data in a reasonable amount of ...
uhoh's user avatar
  • 2,054
3 votes
1 answer
991 views

Why Windows is not showing in the Dual-Boot menu and boot into Ubuntu directly? [closed]

It's been more than a month that I installed Ubuntu 20.04 on a desktop along side with windows (Probably 10 or 11) that was already on the desktop. Now I noticed that the computer boot directly into ...
Camilla's user avatar
  • 2,209
7 votes
3 answers
202 views

What would be the preferred format for a geometry database?

Introduction (analogy to basis set database files) Many programs have a database of basis sets stored in a file such as the following (so that users can just specify in their input file something like ...
Nike Dattani - No Free Time's user avatar
6 votes
1 answer
698 views

How can I predict the time of a simulation using Quantum ESPRESSO?

I performed a vc-relax calculation with hybrid functional on a 2 atoms material using the command ...
Camilla's user avatar
  • 2,209
7 votes
1 answer
2k views

How do I install Quantum ESPRESSO on Linux?

People, can someone please help me how to solve this problem with QE 7.0 installation:
Everson Gomes's user avatar
3 votes
0 answers
321 views

How can we build a polymer from a monomer in Avogadro? [closed]

I have been trying to reproduce a geometry optimization from a research paper, where it was done by Avogadro. However, I cannot find the option for building a polymer from a monomer. I am using ...
Unni Krishnan's user avatar
4 votes
1 answer
778 views

Does anyone know where and how I can download and install Spartan (the Molecular Modeling software)?

I've been given the task to calculate the energy of the lowest unoccupied molecular orbital (eLUMO) using Spartan but I'm not really familiar with the said software, can anyone tell me a bit of an ...
Ellie's user avatar
  • 41
7 votes
3 answers
1k views

Print chemical formula from list of atoms in Python?

Lets consider the following code which uses the Mole object: ...
Nike Dattani - No Free Time's user avatar
5 votes
1 answer
210 views

MOLPRO: is there an analogue of the Gaussian FCHK file?

With the Gaussian quantum chemistry program, I usually generate formatted checkpoint files (.fchk) that I then use to perform different atom-in-molecule analyses. I am currently facing the need of ...
wolfram's user avatar
  • 151
5 votes
1 answer
323 views

What is a good software for computational electrochemistry?

I am thinking about working on computational electrochemistry for a limited subject and don't have a huge amount of time I can invest to explore different software. The JDFTx software seems like a ...
Elie H's user avatar
  • 1,411
4 votes
1 answer
153 views

How to simulate on a computer dissolution of one substance by another?

Is there any publicly available software to simulate this or some other method to see if one substance can be dissolved by the other (and preferably to see how fast)?
user avatar
1 vote
1 answer
75 views

How do I install the beta5 version of PSI4 on my WebMO Basic server?

Installing the basic version of PSI4 on my personal LG Gram 360 (with a Windows OS), used as a my-own WebMO Basic server, was done according to the WebMO tutorial. I then tried to compute the energy ...
Kanghun Kim's user avatar
13 votes
3 answers
257 views

Improving my programming for computational chemistry/physics

What are some good textbooks or online resources to improve my skills in C++, C and Fortran, specifically for computational chemistry. For example, I am interested in learning about parallelisation ...
Fracton's user avatar
  • 271

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