Questions tagged [software-assistance]

Questions asking for assistance with the use or compilation of a software.

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15
votes
2answers
738 views

Open Source PyMol Conda Package: UnsatisfiableError

I'm having an issue installing the open-source version of Pymol using Anaconda on Windows. I have Python3.8.3 installed and when I try add the package with Conda using ...
11
votes
2answers
234 views

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

I am using ASE to write an xyz file. Each frame in the file has a different PBC (periodic boundary condition). Currently, a frame starts like this: ...
11
votes
1answer
60 views

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

I have been using both Gaussian09 and Gaussian16 recently to optimize some metal complexes. The Gaussian manual (for both versions) indicates that the maximum number of steps in a geometry ...
11
votes
1answer
143 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 ...
11
votes
1answer
78 views

Unable to recreate data for benzene from paper in GROMACS 2020.5

I have been trying to simulate benzene in OPLSS-AA forcefield as per this paper: https://pubs.acs.org/doi/10.1021/ct2002122. I have been at a loss, since I believe I have everything running as per the ...
11
votes
0answers
114 views

I ran TDDFT on some small molecules. For some files, the ORCA output files cut short and contain no absorption data. What could be the reason? [closed]

Below is just the end of the output file, and the top of the input file. This is for the molecule FDICTF. The calculation did not run out of time. I ran a batch of 15 molecules, all with same ...
11
votes
0answers
103 views

Setting multiple new atype/dtype/itype with LAMMPS fix bond/create [closed]

When creating a new bond in a LAMMPS simulation with the command fix/bond create it is likely new angles/dihedrals/impropers be need to be set. This can be done with the atype/dtype/itype arguments ...
10
votes
1answer
56 views

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

What's the most efficient way to get the equilibrium phases and phase fractions for a set of alloy compositions? For context, I'm coming from Thermo-Calc/TC-Python where I would just loop through the ...
9
votes
1answer
80 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. ...
8
votes
1answer
115 views

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

I am trying to perform NBO analysis with relaxed density matrix with the open-source program JANPA. I am following the guide here. The first step is to get the NBO input .47 file from Orca v4.2.1. The ...
8
votes
1answer
54 views

How to solve this Bandup software problem?

I have compiled the Bandup software using this command : ./build -compiler gfortran. After that, I tried to follow the tutorial inside the directory ...
8
votes
2answers
89 views

Vacancy with USPEX

I am using USPEX code. I would like to create structures with vacancies. I defined in the file "INPUT.txt" vacancy as Vc, but it stopped and said: ...
8
votes
1answer
140 views

Modelling water using the TIP3P flexible system [closed]

I am modelling water using a TIP3P flexible system. I am using the pair, bond and angle parameters given on the LAMMPS webpage. I am trying to run an $NPT$ simulation at $298\,K$ and $1 \,\mathrm{atm}$...
7
votes
1answer
118 views

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

Regarding input generators for a Linux (Linux Mint 20.1 Xfce) version of Avogadro2, I have managed to get this working using the Flatpak version and copying the input generator python scripts from ...
7
votes
2answers
69 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 ...
7
votes
1answer
105 views

How to sort using ase.build.sort?

I am trying to sort a set of Cu atoms in a fcc (non primitive) crystal structure according to their Z cordinate. I am using ase.build.sort to do this with the help ...
7
votes
1answer
92 views

Reading in E-field with CP2K

I have figured out a way to input a custom electric field in a .cube format, but I am not sure I am doing it in the proper way. Currently my file contains information for the magnitude of the electric ...
7
votes
0answers
214 views

Calculating band structure with HSE using Open_grid (Quantum ESPRESSO) [closed]

I have executed the SCF calculation and obtained the results. After which I used kmesh.pl to extract k-points. I was able to run wannier calculations but there was an error Checking info from wannier....
6
votes
2answers
179 views

Excited state normal mode frequency doesn't match for NH3

I am trying to optimize the geometry of excited state NH3 and get the corresponding normal modes for excited states. I am trying to get the frequencies as mentioned in this reference. They claim to ...
6
votes
1answer
129 views

Pycalphad “Failed while parsing” Yttrium from light alloys database

The code in question is just 2 lines used to import the "COST507 database for light alloys" (downloaded from the opencalphad homepage http://www.opencalphad.com/). ...
6
votes
0answers
72 views

Why does Thermo-Calc one axis equilibrium calculation get stuck in never ending loop? [closed]

I've been trying to run a Thermo-Calc one axis equilibrium calculation on some quaternary alloys in the TCHEA4 database. Most of the calculations work fine, but for some alloys it gets stuck in a loop ...
5
votes
1answer
127 views

How to calculate RMSD with GLIDE?

I need to calculate the RMSD between a co-crystallized ligand and my ligands and a non-co-crystallized ligand with GLIDE but I don't know how. Could someone explain to me how to do it? Many thanks in ...
5
votes
0answers
23 views
5
votes
0answers
60 views

Cannot import both numpy and LAMMPS to python after installing with conda

I installed the module LAMMPS by using this command conda install -c conda-forge lammps I want to import LAMMPS to python code, but it says: ...
5
votes
0answers
63 views

Q-Chem gives “Hessian Appears to have all zero or negative eigenvalues” error when calculating Frequencies [closed]

I have troubles with obtaining spectra for selected molecules in different DFT functionals. I calculate IR spectra for my target molecules (gold complexes with C/H/N/O/S/Au composition) to find how ...
5
votes
0answers
90 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. ...
4
votes
1answer
48 views

PySCF: 2-index and 3-index matrix

The 4-index 2-electron integral can be obtained for the He atom with the following code: ...
3
votes
0answers
25 views

Error while band structure calculation in Quantum ESPRESSO

I have been using BURAI GUI of Quantum ESPRESSO to calculate the optical properties of ZnSe quantum dots. But first I wanted to calculate the electronic band structure. After running the calculation ...