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Questions tagged [software]

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

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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 ...
DC Y's user avatar
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12 votes
0 answers
92 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 ...
user32052's user avatar
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7 votes
0 answers
411 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:/...
logical x 2's user avatar
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7 votes
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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 ...
D.I. Solonenko's user avatar
6 votes
0 answers
544 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 ...
Avishai Barnoy's user avatar
6 votes
0 answers
630 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: ...
theozh's user avatar
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6 votes
0 answers
895 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 ....
khaverim's user avatar
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6 votes
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251 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 ...
Glenn Howes's user avatar
5 votes
0 answers
221 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 ...
Till's user avatar
  • 179
5 votes
0 answers
76 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 ...
Eenoku's user avatar
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5 votes
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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 ...
user34801's user avatar
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4 votes
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247 views

Is There a Problem with the Assignment of Stereochemical Descriptors by ChemDraw in Select Examples?

While using ChemDraw Professional 21.0.0.28 to construct some cyclic allenes and rotationally restricted biphenyls, I came across anomalous assignments of stereochemistry. [For the latest version of ...
user55119's user avatar
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4 votes
0 answers
152 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 ...
Max's user avatar
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4 votes
0 answers
317 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. ...
Vladislav Gladkikh's user avatar
4 votes
0 answers
151 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 ...
AlyChem's user avatar
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4 votes
0 answers
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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 ...
AlanZ2223's user avatar
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4 votes
0 answers
802 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: ...
tmartin's user avatar
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3 votes
0 answers
20 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 ...
wulf123's user avatar
  • 31
3 votes
0 answers
83 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 ...
jheindel's user avatar
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3 votes
0 answers
718 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 ...
Yoda's user avatar
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3 votes
0 answers
3k 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 ...
Justanotherchemist's user avatar
3 votes
0 answers
265 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 ...
X Zhang's user avatar
  • 57
3 votes
0 answers
203 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 (...
user4779's user avatar
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3 votes
0 answers
167 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 ...
Josh Pinto's user avatar
  • 2,461
2 votes
0 answers
39 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 ...
dtg67's user avatar
  • 41
2 votes
0 answers
776 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: ...
Ignas Pakamorė's user avatar
2 votes
0 answers
68 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 ...
浪川菜奈's user avatar
2 votes
0 answers
252 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 ...
Baris Vvolf's user avatar
2 votes
0 answers
222 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 ...
Tyberius's user avatar
  • 11.8k
2 votes
0 answers
87 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 ...
Eenoku's user avatar
  • 1,267
2 votes
0 answers
231 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 ...
Stanislav Bashkyrtsev's user avatar
2 votes
0 answers
120 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 ...
Greg's user avatar
  • 5,365
2 votes
0 answers
278 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 ...
user3587374's user avatar
2 votes
0 answers
85 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 ...
hamidmehdipour's user avatar
2 votes
0 answers
95 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 ...
d.conors's user avatar
2 votes
0 answers
121 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 ...
M. Obies's user avatar
  • 109
2 votes
0 answers
180 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?
M. Obies's user avatar
  • 109
1 vote
0 answers
66 views

"Is there any library in Python or software for analyzing raw chromatography data?"

I have taken the data directly from the FID sensor using a DAQ, so I have the chromatography data in this format: (2 data colummns in a txt file) (18000 rows) Time (s) Intensity (V) 0.00367___0.0008 ...
user138375's user avatar
1 vote
0 answers
61 views

Hartree-Fock calculations of the states of Nitrogen molecule ion

I was reading the third chapter of "Modern Quantum Chemistry" by A. Szabo and N. Ostlund about HF calculations, and in the end of the chapter it shows as an example a calculation on $\ce{N2}$...
AlfredV's user avatar
  • 461
1 vote
0 answers
157 views

Gibbs Free Energy for solvation using Gaussian09

I am trying to compute the $\Delta G$ for the solvation of a molecule using the continuum dielectric model in Gaussian09. Following the recomendation in the manual of the software, I am using the SMD (...
AlfredV's user avatar
  • 461
1 vote
0 answers
23 views

Software for running dynamics simulation of polymeric and mixed biomaterial (e.g hydrogels)

I was working on the development of a soft solid hydrogel having polymeric chains and molecules of different compounds dissolved in Phosphate Buffered Saline solution. There is a sub-study regarding ...
Syed Hasan Sarwar's user avatar
1 vote
0 answers
1k views

Full list of CAS numbers?

I'm trying to find a full list of CAS Registry Numbers, but it looks like it's not in open access. Is it a proprietary database that can't be downloaded easily?
Stefan Smirnov's user avatar
1 vote
0 answers
43 views

How can I save an EEM file on a Fluoromax4?

I'm trying to run excitation-emission matrices on some water samples, but I'm running into some software issues that the manuals aren't helpful for. In order to use R studio to extract my data, I need ...
dogman's user avatar
  • 61
1 vote
0 answers
44 views

Is there a computer program capable of showing protein conformational changes based on pH?

As it is known, changes in pH change the attractions between the groups in the side chains of the protein. Acidification can, for example, cause protonation of the $\ce{COO-}$ end to $\ce{COOH},$ ...
RoyBatty's user avatar
  • 111
1 vote
0 answers
111 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 ...
wulf's user avatar
  • 93
1 vote
0 answers
50 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 ...
Flyingfenix's user avatar
1 vote
0 answers
802 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 ...
Andrea's user avatar
  • 261
1 vote
0 answers
148 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 ...
ksousa's user avatar
  • 663
1 vote
0 answers
61 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 ...
Tan Yong Boon's user avatar
1 vote
0 answers
639 views

How to interpret Gaussian output for excited states?

I have calculated the excited energies for benzene in Gaussian. The output therefore was: ...
p_punkt's user avatar
  • 369