11

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 is only compatible with standard XYZ format. Also, take a look at this answer (to another question) about adding PBC info in VMD after loading standard XYZ ...


10

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 packager. Anyway, we are looking into that, but will probably take some time, since there is no detail error for us to work with at the moment. I suspect that ...


9

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 scientific packages, including PyMol. I was able to find a Windows version for Python 3.8 pymol‑2.5.0a0‑cp38‑cp38‑win_amd64.whl and after downloading this file, I was ...


9

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 info you can follow this link: https://pymolwiki.org/index.php/Linux_Install Hope this helps :)


9

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 unclear for me (please give me some advice), in what form should these scans be visualized: colored map, or 3-d surface which can be rotated, or simply the ...


8

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 z position of all atoms. from ase.build import bulk, surface from ase.build.tools import sort Cu = ase.build.bulk('Cu', 'fcc', a=3.6, cubic=True) surface = ase.build.surface(Cu, (1,1,1), 4, ...


8

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 corrections: Changed ELEMENT Y HCP_A3 8.89059+01 5.9664E+03 4.4434E+01 ! to ELEMENT Y HCP_A3 8.89059E+01 5.9664E+03 4.4434E+01 (adding E to the exponent of the mass) ...


8

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 opt(maxcycle=N) can only set the max value within this range, but not any higher. IOP(1/152=N) changes this internal max value, allowing maxcycle to be raised as ...


7

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 geometries. These are the results of the Franck-Condon approximation, which says that there is a high probability that a molecule is near its equilibrium geometry, ...


7

Please, check the version of OpenBabel you are using. At least, version 3.1.0 has the pdbqt format implemented: # obabel -v No input file or format spec or possibly a misplaced option. Most options must come after the input files. (-i -o -O -m can be anywhwere.) Open Babel 3.1.0 -- Jan 11 2021 -- 11:51:22 and: # obabel -L formats abinit -- ABINIT Output ...


6

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 match the values one gets from the inbuilt function. In any case, calculating RMSF for just the C alpha atoms gives more information about the structural changes ...


6

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


6

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 line yourself. I am no tcl expert but here is an example that works for me: set filename [lindex $argv 0] # load the coordinates into vmd mol new $...


6

You likely need to ensure the correct anaconda environment is loaded. Use the following to get a 2.7 environment. conda create --name py2 python=2.7 conda activate 2.7 pip install ase==3.12.0 Your problems probably stem from issues with pip or the location of the installation. Use this method to ensure you have your 2.7 environment and you have ase in it. ...


6

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 compositions. In that case, it is easy and faster to let pycalphad broadcast the conditions for you. It will skip any conditions that have independent mole ...


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 different charges on the C and H atoms in my simulation as in the paper. I did not think to check LigParGen's output, and that is my own fault. Also, I was using ...


5

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 than 0.01 Bohr as this corresponds to about 0.005 angstroms. While I think this is a weird limitation to exist, you may consider that this is such a small distance ...


5

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 Long answer: First of all I would advise you to go through the manual of GAMESS. There are lots of problems in the input file, and most of them can be easily ...


5

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 $\ce{NH3}$ is a fairly small molecule, though I don't know how time consuming this will be relative to your initial CCD calculation. TZV != TZVPP. The def2-TZVPP basis ...


4

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 that PR, and it should work. If it does not, please report the problem in the comments to that pull request. You can also ask questions related to the Bandup ...


4

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 applying laser pulses and that you should use EXTERNAL_POTENTIAL instead, with the READ_FROM_CUBE option. Not sure whether printing the imposed potential is possible, but you could print the ...


3

All keywords in Gaussian (effectively) only accept integers as arguments. Keywords are all translated into IOps (Internal Options), which are written in the format IOp(overlay/option=value) where value is always an integer. This seems to have been an early design decision to only allow integer valued options and while Gaussian is open to adding/deprecating ...


3

(Source: this question about point defects on the USPEX google group.) This seems like a restricted crystal structure prediction problem since knowing the crystal structure of the system beforehand becomes a requirement. You must specify a space group (or other symmetry groups like the point, layer, etc groups) via the symmetries tag in the INPUT.txt file. ...


3

In the density fitting / resolution-of-the-identity (RI) formalism, a two-electron integral $(ij|kl)$ in the atomic-orbital basis is approximated as $(ij|kl) \approx \sum_{PQ} (ij|P) (P|Q)^{-1} (Q|kl)$ where $P$ and $Q$ are auxiliary functions, and $(P|Q)^{-1}$ is the inverse Coulomb overlap matrix. The RI expression can be written in a form that resembles ...


3

The software GLIDE is not used for RMSD calculation. GLIDE is dedicated to do small ligand/protein docking (rigid/rigid and flexible/rigid). You can calculate the RMSD by hand, using MAESTRO, CHIMERA and VMD interfaces (all free for academics) among many other software (also free).


2

Go here, no need to install, use on the web http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html


2

The author seems to have abandoned this question but I will summarize what the comments are saying. It seems this issue was likely related to the cutoff applied to the TIP3P model. This resulted in pressure and density values that were incorrect. Since the author was doing an NPT simulation and reported an incorrect pressure was seen (the average pressure ...


1

I never have used USPEX, but here is a bad solution to the problem even if it doesn't support vacancies. Use a dummy element such as Na that is not in your system. Post-process the structure afterwards to remove it, using something like ASE. This is definitely not ideal, but you might find that it works to generate reasonable structures. USPEX might use ...


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