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OpenMOLCAS
MOLCAS is now in it's 5th decade! The first version was written in the 1980s by the group of Bjorn Roos, one of history's giants in quantum chemistry. It can do many of the things most mainstream quantum chemistry packages can do: integrals, Hartree-Fock, DFT, MP2, coupled cluster, geometry optimization, etc., and while it can do "single-...
20
ORCA
Official website: https://orcaforum.kofo.mpg.de/app.php/portal
What is ORCA?
ORCA is a general-purpose quantum chemistry program package that features virtually all modern electronic structure methods (density functional theory, many-body perturbation, and coupled-cluster theories, and multireference and semiempirical methods). It is a flexible, ...
18
I've never done this myself, and there may be other approaches, but one possible detailed answer seems to be provided by the Gaussian webpage. For stability reasons, you can find this page via the Internet Archive (pdf).
In particular, you may want to jump to the sections
"Determine the principal axes of inertia"
and
"Generate coordinates in the rotating ...
15
Psi4
Psi4 is a fully open-source quantum chemistry package that is gaining a lot of interest in my community (computational) combustion chemistry.
Here is the manual for the latest release: it has most, if not all, of the theoretical methods (HF, DFT, CC,...) and also lots of interfaces and integrates into C++ and Python (sadly no Fortran).
The bonus on it ...
14
GAMESS
For many researchers, GAMESS is the "natural" substitute for GAUSSIAN. Developed and maintained by the group of prof. Gordon (also a banned GAUSSIAN user, see image below).
Official website: https://www.msg.chem.iastate.edu/gamess/index.html
What is GAMESS:
GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can ...
13
Ah, yes, the fun of force-field building.
For the answer to a simple geometry optimization, see I. Camps response below.
Skip to the end if you want what is a more general answer to building an entire force-field. Read the whole thing if you want some insight into force-fields, particularly partial charges.
First, doing an electronic structure calculation (...
12
Band structure is a concept for periodic system only. As proteins are not periodic structures, they don't have electronic bands.
The fact that you can download a PDB file (or a CIF file) with information about the crystal, it is just due to one of the ways we found to determine the protein structure that is crystalizing the protein and then using single ...
11
It's not a descriptive error message, but this occurs when you reach the max number of iterations for the Eigenvector Following (EF) algorithm and still haven't converged a lambda. While Gaussian uses a different approach (the Berny Algorithm) for methods which have analytical gradients, CCSD(T) is one of the few methods for which these still aren't ...
11
Basis set name versus number of total orbitals
I would like to first address a part of the question that appears to be a misconception about the use of a 6-31+G(d,p) basis set, since you wrote:
"In my understanding of such basis sets, it is difficult to do this."
6-31+G(d,p) is not a "big" or "small" basis set, unless we're ...
10
This is a very general answer, but let me point you in the right direction at least. If you are looking at a molecular system such as C6H6, you will likely want to use a non-periodic code such as Gaussian. This page describes many different methods of charge analysis and you can use this information to calculate charge transfer complexes and local charges on ...
10
The canonical source is probably Gaussian's user documentation according to which the cube file defines an initial point $(x_0, y_0, z_0)$, as well as three step directions $(x_i, y_i, z_i)$ and the corresponding number of steps $N_i$ for $i=1,2,3$. The data are computed at the gridpoints, since averaging would make grid data evaluation much more costly, and ...
10
The Jmol software is able to plot different surfaces.
In the example below, the system is a Mobius strip and the ESP was calculated using MOPAC but as Jmol is full compatible with Gaussian outputs, I think there will be no problem.
Mobius strip structure:
Mobius solvent-accessible surface (SAS):
Mobius electrostatic potential mapped on solvent-accessible ...
10
All Gaussian jobs when completed without any error, will have, at the end of the output file, a phrase/thought/quote from someone famous. It is kind off an easteregg. My latest Gaussian successful job finished with this quote:
THERE IS NO SCIENCE WITHOUT FANCY, NOR ART WITHOUT FACTS.
-- VLADIMIR NABAKOV
Anyway, answering your second question:
What ...
10
You are probably running a combined optimisation and frequency job in Gaussian. (I discourage that, but that's a different issue.)
The line means that the calculation preceding it has been run as a test calculation, see https://gaussian.com/test. An archive entry has not been created. The reasons may be multiple and depend on the actual input file. That's ...
9
A periodic boundary condition creates a box around your molecule (or surface) and then treats the molecule leaving the box on the right side as entering the box from the left. This is particularly useful for surfaces as otherwise the atoms at the edges (but not on top where you'd be exposed to a solvent) would otherwise degrade into open space. This ...
9
I have yet to find a source that lays this out explicitly, but from the examples I could find, it is not too hard to infer the meaning of these sections.
To start with (and possibly point you in the right direction to look for more information), this type of *.wfn file was developed as the input format for AIMPAC and quickly spread to be used as an output ...
8
General vs segmented contraction
Unless one is using a fully decontracted a.k.a "primitive" basis set, one uses contracted Gaussian-type orbitals (cGTOs), which are given as a linear combination of the primitive Gaussian-type orbitals (pGTOs):
$\chi_i^\text{cGTO}({\bf r}) = \sum_{\alpha} d_{\alpha i} \chi_\alpha^\text{pGTO}({\bf r}) $.
...
8
Integral Screening
It is possible to place upper bounds on integrals based on the Cauchy-Schwartz inequality:
$$
\left( a a | b b \right) \ge \left( a c | b d \right)
$$
If the first integral is computed and deemed insignificant, the latter is as well. One can further combine this with the appropriate density matrix element and decide that the resulting ...
8
There are several protocols. Since you mention that you're mostly looking for trends, I'll give the faster method, e.g. by Jason Gilmore:
"Expanding and Testing a Computational Method for Predicting the Ground State Reduction Potentials of Organic Molecules on the Basis of Empirical Correlation to Experiment"
J. Org. Chem. 2012, 77, 15, 6423–6430
...
8
Complementing the answer by @Tristan, in this question you will find the several methods used to determine the atomic charges.
Also, you can use Gaussian to calculate/export the wavefunction and them use Multiwfn package to estimate the system charges using several approaches:
Population analysis. Hirshfeld, Hirshfeld-I, VDD, Mulliken, Löwdin,
Modified ...
8
The Karlsruhe def2 basis sets cover most of the periodic table and are based on effective core potentials for relativistic effects; these are a good starting point for whatever you are interested in, and are also available built-in in Gaussian.
As to the functional, since you want to study slabs you probably want to use a pure functional since otherwise the ...
8
I am not very well versed with ONIOM calculations, so I cannot really comment, whether my following examples are actually sensible, I just picked your example with different methods.
I think the biggest problem here is the lack of a real description of ONIOM for Gaussian, especially when it comes to defining general basis sets. Long story short, and if you ...
8
Since you include the command cphf=RdFreq, Gaussian expects you to have entered a perturbation frequency after the rest of the input. You need to specify a frequency in order to compute dynamic properties. Here is how it would look for your case. Note you can specify the perturbation in a couple different units (nm, au,etc).
--Link1--
%chk=go40r.chk
%nproc=...
8
I recently had the same question. After emailing Gaussian support I was informed that the units are indeed $\sqrt{\text{km}/\text{mol}}$. From their reply I also believe that the derivatives are calculated with respect to the 3N-6 vibrational modes obtained through the application of the Sayvetz conditions as detailed in their whitepaper (Paragraph after Eqn....
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
Multiwfn
Multiwfn is a great tool for cube file analysis and wfn file analysis that can probably do almost everything you want to do. It is capable of doing math between cube files, outputting that file and then continuing to do more math. I believe it also allows for custom formulas to be input into the source code in some straightforward way (I have ...
7
I'm surprised that a single geometry step could result in a converged structure that's 15 kcal/mol lower in energy. That is odd, although not impossible. I would recommend carrying out a frequency calculation on the structure. It should, of course, have no imaginary modes. I'd also consider running a "regular" geometry optimization on the resulting ...
7
Van der Waal's radii for all atoms in the molecule are required to compute the dispersion for $\omega$B97X-D (this is also true for Grimme's dispersion). Unfortunately, Gaussian09 doesn't seem to have the radius for $\ce{Au}$ and it is also not possible to manually enter it through the input file. The radii for the elements up through $\ce{Rn}$ (atomic ...
6
TheoDORE
Dealing with cube files is fairly easy as long as they all have the same grid definition. A cube file is basically just a long vector of numbers and you can add and multiply them as you wish. You can for example check lib_util.py of the TheoDORE package. This might do what you want in a simple scriptable form. Maybe the lin_comb routine does what ...
6
MOLPRO
Continuing Susi's excellent benchmarking for $\ce{Zn}$ and $\ce{Zn_2}$, MOLPRO 2012 gives for $\ce{Zn}$:
RHF-SCF energy: -1777.84665521
CPU time for INT: 0.42 SEC
CPU time for RHF: 0.01 SEC
Disk used for INT: 12.87 MB
However the RHF energy was converged already at iteration 1, so there wasn't much work to do:
ITERATION DDIFF ...
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