Questions tagged [software]

For questions pertaining to software used by chemists for professional or academic purposes.

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11
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84 views

Is there a structured data source containing information on the World Health Organisation's Stability Testing Policies?

Hoping to automate some product testing guidance software, I've been attempting to find a (hopefully live, up-to-date) Database, Web-service, or other structured data source containing the ...
10
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635 views

Understanding two-electron integrals in Gaussian 09

I was comparing the two-electron integrals (electron repulsion integrals, ERI) printed by various well-established packages (Gaussian, GAMESS, Molpro etc.) and observed that Gaussian is the oddball in ...
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352 views

Cloud-based molecular modeling software

I’m an IT Acquisitions and Licensing specialist researching well-supported cloud software alternatives to Fujitsu’s molecular modeling SCiGRESS. I am coming in with a tech background, but little to ...
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0answers
314 views

How are the angle bending parameters defined in the MM2 force field?

I am currently looking through the openbabel implementation of the mm2 forcefield. While I understand most of the implementation, I don't get the definition of the angle bending parameters (see https:/...
6
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158 views

How to extract force constants for normal modes from ORCA?

I am following the computational method described in Scientific Reports.[1] Where the authors analyze the contribution of each excited state normal-modes to the shift of the transition energy. For ...
6
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0answers
297 views

OpenBabel: how to get correct SMILES from Gaussian output?

I would like to get the molecular structure as SMILES from Gaussian output files. OpenBabel seems to be the tool made for such tasks. However, the structure is not always correct. One example: ...
6
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688 views

Molecular visualization software for Raspberry Pi?

I've been using our lab's code MCMD on my Raspberry Pi for fun and exploratory purposes. I'm trying to find a VMD, Avogadro, Ovito, or other equivalent that is usable on Raspberry Pi, e.g. to view ....
6
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0answers
2k views

Warning during geometry optimization via Gaussian

I have some recurrent problem with my DFT calculations [functional: hseh1pbe; basis:6-31+g(d,p), object: porphyrin derivative]. During the MO setting I get: **** Warning!!: The largest alpha MO ...
5
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0answers
69 views

How do I display a potential energy surface with molden?

I calculated a gaussian scan job for propylcyclohexane with two dihedral angles. Now I want to display a potential energy surface for that molecule with molden. I am new to molden and only found the ...
5
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0answers
61 views

Software for computations of rovibrational states' energies and corresponding spectroscopic constants in diatomic molecules

I need to compute rovibrational energy levels and also the spectroscopic constants, especially $\omega_e$ to compare my results with other papers. So far I've tried LEVEL16, which seems very ...
5
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0answers
168 views

Ab initio MD simulations in VASP

I'm not sure if this is an appropriate question for Chemistry.SE, but I'm taking a stab. I'm running ab initio MD calculations in VASP and I'm trying to optimize different input tags. On the VASP ...
5
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0answers
118 views

What are the essential arrows for entering chemical equations in text?

I'm the author of a custom chemistry keyboard on iOS. I am looking at improving the selection of Unicode arrows I can provide. When the device is a phone in portrait mode, I don't have a lot of extra ...
4
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72 views

How can I save and read the CI vector during CASSCF calculations in Gaussian?

I have searched through the GAUSSIAN 16 manual and have not been able to solve these two related issues: (1) I want to be able to save the CI vector and load it as an initial guess for a different ...
4
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259 views

How to get the second electron affinity of tellurium?

I need the value of the second electron affinity of Te, i.e. the energy change associated with the attachment of an electron to a $\ce{Te-}$ anion $$\ce{Te- + e- -> Te^{2-}}$$ In the books (e.g. J. ...
4
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141 views

What computational methods are available for predicting nanoparticle structure?

I'm a quantum chemist, and nearly every system I've ever cared about has been studied by DFT. However, I am currently trying to model the surface interactions on a nanoparticle around 100 nm in ...
4
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700 views

How to Locate the Excited State Dipole Moment in Turbomole Output (TD-DFT)

I want to calculate the dipole moment for the first excited state with a Q.C. program (TURBOMOLE: TD-DFT). The calculation lists the following output: ground state total dipole moment: ...
4
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1answer
329 views

How to measure a distance along the surface of a protein in a PDB

I would like to measure the distance between two active sites in a protein complex (pdb), but I do not find a straightforward way to do it. To be more precise I need the distance along the surface ...
3
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13 views

Correlating specific heat (Cp) of a substance with other substance on the basis of similar physio-chemical properties

I am modelling $\ce{H2O2}$ decomposition in ANSYS Chemkin-Pro and I have difficulty finding $C_p$ (specific heat at constant pressure) for liquid $\ce{H2O2}$ for various temperature ranges. My ...
3
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116 views

Is there a Python module for calculating Ovality of a molecule?

Ovality gives a measure of how the shape of a molecule approaches a sphere (at one extreme) or a cigar shape (at the other). Ovality is described by a ratio of volume to area (see https://en.wikipedia....
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40 views

How does one calculate the electronic difference density in practice?

I am interested in calculating electronic difference density maps. These have been described for quite a long time by Bader and others. For example, below is the fourth of a series of papers which ...
3
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0answers
56 views

Sources for files for testing a thermal ellipsoid (ORTEP) program

I am trying to reimplement the functionality of the classical program ORTEP for producing thermal ellipsoid plots of a crystal/molecule in a modern computer language. Unfortunately, I am having ...
3
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0answers
455 views

Restarting a Gaussian partially constrained relaxed surface scan using GICs

I am Using Gaussian 16 rev D.01, and I want to perform relaxed surface scans where I vary a bond distance. At the same time I constrain seven atom coordinates during the entire optimization (this is ...
3
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0answers
972 views

Predict polarity (TLC, column) using ChemSketch (-Draw)

I'm currently working on a project where I have to make and isolate often quite similar molecules. But, as I change the functional groups the overall electronic situation and polarity of the product ...
3
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0answers
216 views

Transition state search for rotational motion

This question is regarding Gaussian Computational software package. I have a system where one product forms from one conformational arrangement of molecular intermediate (conformational minimum) and ...
3
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0answers
77 views

Is it possible to “brute-force” material creation through algorithms?

I know its a bit of a soft question, but lately I've wondered what important properties and calculations would a program that iterates through certain types of molecules and atoms need in order to ...
3
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0answers
173 views

Cis/Trans-Decalin in ChemBio3D

According to my organic chemistry textbook, Cis-Decalin has the two rings nearly perpendicular to one another, with the middle hydrogens cis to one another. Trans-Decalin has the ring nearly flat (...
3
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0answers
146 views

How can I get ChemSketch to get N and H atoms closer while still operating in ACS style and without adjusting atom sizes?

A person at wikipedia is getting on my case for creating this image because the N and H symbols are so separated even though this seems to be the default of ChemSketch (one of the softwares that's ...
2
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0answers
20 views

CP2K Spherical Cell

I'm trying to run a gas phase cluster calculation in CP2K. I want to create an outside force to constrain water molecules that are in the simulation within a radius of a central ion. I want to create ...
2
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0answers
79 views

What are the alternatives we have to the VEDA 4 vibrational energy distribution analysis software?

Said software is very useful when you need to assign the peaks in vibrational spectra to different vibrational modes found in a hessian calculation for a given molecule, as described in Jamróz, Michał ...
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0answers
50 views

Rotating dihedral and Angles And Generate File For Each Degree

I need to optimize a force field I generated. For this, I should apply Genetic Algorithm (G.A). To apply G.A I should do this for 220 molecules: 1) Find all dihedrals for each molecule ( I did this ...
2
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0answers
153 views

DFT Exchange-Correlation Two Electron Integrals

Are there any electronic structure programs that print the exchange-correlation (XC) integrals for a given DFT functional? These integrals are of the form $$\langle pq|w|rs\rangle$$ where $w$ is an XC ...
2
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0answers
56 views

How to obtain spectroscopic constants Omega_e, Alpha_e, B_e, D_e and D_0 from centrifugal constants?

I need to compute a spectroscopic constants of $N_2^+$ states and I would like to do it using LEVEL16 software, due to its high interpolation flexibility. But it seems, that LEVEL16 can only compute ...
2
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0answers
110 views

ApexTrack: peak tail looks like a shoulder

I'm trying to implement ApexTrack algorithm in my software by following the description written by Waters. But many chromatograms that I see have noticeable tailing of peaks: . No matter what ...
2
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0answers
86 views

Generating density matrix of a wavefunction from common quantum chemistry software

I am looking for density matrixes for a couple of closed shell and open-shell systems, and I wonder if there is a trivial way to make e.g. Gaussian just generate an output for me. I may be wrong but ...
2
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0answers
49 views

Geometry optimisation in Gaussian09

I have looked at various sources regarding this, including the Gaussian official website. However, I have not managed to understand the geometry optimisation method used by Gaussian, a method known as ...
2
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0answers
157 views

Rendering software for publication

Does anyone know how I can render chemical structures of small organic molecules to look like the below images? I have been looking around, and I cannot seem to find an answer. The closest lead I ...
2
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0answers
71 views

Setting to basis set for electron transfer in type II CdS/TiO2 heterostructre for PYXAID package

I am studying electron injection from $\ce{CdS}$ into $\ce{TiO2}$ using NAMD approach. Now I'm using pyxaid package. Would be possible someone kindly help me with construction of basis set for this ...
2
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0answers
74 views

TINKER molecular modeling extra forces - energy unit

I use the TINKER molecular modeling software package (version 7.1.2) for computational physical chemistry. There is an extra file (extra1.f) included for the user to edit and incorporate their own ...
2
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0answers
112 views

MOLCAS CASPT2 energy

I have calculated all the roots for a specific symmetry and I need to calculate the CASPT2 energy for all the roots. For example: here I have 4 roots and I need to calculate the CASPT2 energy for all ...
2
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0answers
99 views

Inactive versus frozen orbitals in CASSCF

Does it make any difference if I use the frozen keyword instead of the inactive keyword in MOLCAS CASSCF calculations?
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16 views

Inputting liquid species in chemkin pro

I have been trying to model various species decomposition/combustion in Chemkin Pro. Chemkin only lets you to allow to input gas phase and surface site solid species in your input files, but I have ...
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0answers
29 views

Suggestions of GHS-compliant labelling software

Having amassed a rather large collection of reagents and products from previous years of chemistry experiments, I find rather annoying that their labels aren't even close to being standardized to the ...
1
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1answer
286 views

An automated approach to visualize several xyz structures

I have several .xyz files (each composed of several molecules) and I'd like to find an automated way to visualize and save them. I'd appreciate any guidance.
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0answers
223 views

How do you optimize an organo-metalic compound containing cerium in in Gaussian?

I am trying to perform optimisation of the molecule attached. I need to get partial charges and frequencies. The issue is that it doesn't converge with following input: ...
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0answers
171 views

How to fix 'error: hangup' in Gaussian 16 modredundant scan calcuation?

I have got a problem during my calculations with Gaussian 16. Everytime I start a job to scan the energy about 2 dihydrals I run into the following Error: hangup. I ...
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0answers
104 views

Valency of each atom in a molecule with python

Consider ethanol, where each carbon atom has a valency of 4 and oxygen a valency of -2. I would like to determine these values for many compounds given their SMILES or InChI keys. (For the purpose of ...
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0answers
328 views

How to interpret Gaussian output for excited states?

I have calculated the excited energies for benzene in Gaussian. The output therefore was: ...
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0answers
171 views

How does the “sample type” selection on the MassHunter software for Agilent 7900 ICP-MS affect the quantitative results?

I'm new to using the instrument, and recently I have tried to measure Cr in both the eluent(1% nitric acid) and a method blank (also 1% nitric acid, but after it has gone through the entire analytical ...
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0answers
38 views

Detect the presence of non stereochemically annotated atoms in mol files

I'm facing a problem now and I don't know where to start from. I'm treating databases in which there are mol-files that have stereo-chemical carbons, which, sometime, are not annotated as being R/S or ...
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0answers
52 views

Is there a generic graphical language to represent chemical reactions?

I want to show a schematic representation of chemical reactions from start to finish in a way that will include more detailed preparation instructions than a plain chemical formula: volumes, ...