11 votes

How to include individual PBC box dimensions in xyz file format compatible with VMD

That is a modification of the standard XYZ file format and is called extended XYZ format, and not all programs are compatible with it. From the VMD Molfile Plugin Documentation page, it looks that VMD ...
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  • 19k
10 votes

Avogadro for Linux -- Input Generators and Submitting Job to QM software?

I am the person who package Avogadro2 as Flatpak. Stumble upon this thread randomly. I was not aware about this issue when I just randomly clicking on things. Not Avogadro power user, just software ...
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9 votes
Accepted

Why does Gaussian ignore the opt=maxcycles keyword for optimizations?

This requires an additional IOP to do. It seems that Gaussian sets a separate lower and upper bound on the number of optimization steps that will be performed based on the number of coordinates and <...
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  • 14.2k
9 votes
Accepted

Open Source PyMol Conda Package: UnsatisfiableError

I was able to find a workaround to get open source PyMol installed on Windows. Christoph Gohlke at the University of California has a large library of precompiled Python wheel files of various ...
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  • 14.2k
9 votes

Open Source PyMol Conda Package: UnsatisfiableError

If you're using Linux its better if you install such packages using the apt-get method. apt-get install pymol I've encountered a similar error while installing MatPlotLib through conda. For more ...
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  • 4,268
9 votes
Accepted

How to create a Potential Energy Surface in Chemcraft?

I am the author of Chemcraft. Your job contains a 2-dimensional PES scan, and currently Chemcraft can visualize only 1-dimensional scans. I plan to implement support of 2d scans in future. It is ...
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  • 106
8 votes

How to sort using ase.build.sort?

The following code should create a Cu surface and sort it by z index. We do this by providing tags for the positions of the atoms. [:, 2] allows us to select the ...
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8 votes

Emission and absorption UV-Visible spectrum using GAUSSIAN-09

Roughly speaking, absorption spectra are obtained by TDDFT calculations on optimized ground-state geometries, while emission spectra are obtained by TDDFT calculations on optimized excited state ...
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  • 7,223
8 votes
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Pycalphad "Failed while parsing" Yttrium from light alloys database

Thanks to Tyberius for pointing out one issue in the database in their comment. The pycalphad database parser is strict, but also tries to prevent ambiguities or mistakes. I made the following ...
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8 votes

Installing Quantum Espresso on an Apple M1 processor possible?

I was able to replicate your output on a Macbook Pro M1. Therefore, at the moment running ./configure followed by make all is ...
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7 votes
Accepted

Pycalphad most efficient way to gather equilibirum phase data for set of alloy compositions?

In your comment, you mentioned that you may be testing many alloys (100,000s). I will assume that interested in taking more of a screening approach, rather than specifying precisely 100,000 alloys ...
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7 votes
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Converting SDF to PDBQT using OpenBabel

Please, check the version of OpenBabel you are using. At least, version 3.1.0 has the pdbqt format implemented: ...
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  • 19k
7 votes

How do I compile Quantum Espresso with HDF5 support? (Linux)

Here are a few things you could try: ./configure --with-hdf5-libs=<options> --with-hdf5-include=<path> (note the double dashes) ...
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7 votes
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Does SCF calculation have to be done before calculating DOS?

The community wiki by Tyberius is a bit misleading here, you are not doing molecular dynamics calculations (IBRION=0) but likely a geometry optimization (IBRION=1,2,3). In the case of geometry ...
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6 votes
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Calculating RMSF in VMD

The problem in the sript I had written was that my system was not able to handle that many variables at one go. So I made the calculations piecewise i.e. 40 atoms at a time and the results closely ...
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6 votes

How to get the .47 file from ORCA for natural bonding orbital analysis

All files are always created in the run directory where ORCA runs. I specifically did not want to deal with environment variables and path names and all that. Hope that helps! best wishes, Frank Neese
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6 votes

How to include individual PBC box dimensions in xyz file format compatible with VMD

Camps is correct, VMD cannot directly parse the comment line of an xyz file because the extended ASE format is not recognized. You can, however, use a tcl-script to load the file and parse the comment ...
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  • 1,351
6 votes

Downloading ASE (Atomic Simulation Environment) on older versions of Python

You likely need to ensure the correct anaconda environment is loaded. Use the following to get a 2.7 environment. ...
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6 votes

Unable to install P4Vasp

The source code is still available on Github, though it hasn't been updated for nearly 4 years. While the project seems to be abandonded, you should be able to compile from source. I don't suspect the ...
5 votes

How to use fractional numbers as arguments for keywords in Gaussian input?

This is a weird quirk of the Gaussian input and I am unsure why it is implemented this way. The maxstep is given in a unit of 0.01 Bohr and it is presumed you do not wish to use a maxstep of less ...
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5 votes
Accepted

How to use VEDA to analyze vibrational energy distribution?

After some experimentation, I was able to track down the problem. Your output files tell me that you are using Gaussian 16. Upon inspection, the formchk utility in that version seems to put an "...
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  • 556
5 votes
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Unable to recreate data for benzene from paper in GROMACS 2020.5

Thanks to the generous time and comments of @ShoubhikRMaiti, I was able to recreate the simulation. The problem in my code was 2-fold: I was using the topology filed created by LigParGen, which had ...
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  • 3,917
5 votes
Accepted

Excited state normal mode frequency doesn't match for NH3

This is not a full answer, because it does not solve the problem. But I hope to shed some light on why you are not getting the correct frequencies. Short answer: I suspect there is a bug in GAMESS ...
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  • 5,734
5 votes

Excited state normal mode frequency doesn't match for NH3

I can see two major problems: CCD != CC2 and I'm not certain if CC2 is available in GAMESS. CC2 is an approximation of CCSD, which is available in GAMESS. You may be able to use this since $\ce{NH3}$ ...
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  • 14.2k
5 votes

Installing Quantum Espresso on an Apple M1 processor possible?

It looks like Quantum Espresso is available through conda-forge which will be helpful. Conda Forge has worked to migrate many packages to ...
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5 votes
Accepted

What is the detailed difference between Vasp_std and Vasp_ncl?

I don't know any VASP-specific details, but the basic answer is that the three versions are almost identical, and solve the same equations in the same way. If we take vasp_std as the reference, then ...
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  • 3,957
5 votes

Does SCF calculation have to be done before calculating DOS?

In the passage just above what you quoted, it says: For dynamic simulation (IBRION=0), the charge density on the file is the predicted charge density for the next step: i.e. it is compatible with the ...
5 votes

Unable to install P4Vasp

The P4VASP code is one of the easiest visualization tools for VASP outputs that I have been using. From your question, I understand that your system can't find the p4vasp executable file which can be ...
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  • 5,511
4 votes
Accepted

How to solve this Bandup software problem?

I think your problem was solved in this pull request. It is not merged yet because it breaks backward compatibility with python3.6 and lower. But if you use 3.7 or higher, you may try to install from ...
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4 votes

Reading in E-field with CP2K

From looking at the very long wavelength you specified, I assume your intent is to apply a static field to the calculation? I read here that EFIELD is intended for ...
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