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Questions tagged [computational-chemistry]

A field which employs computers to model and study chemical systems and chemical behavior, using various models, from approximations of the Schrödinger equation to Monte-Carlo simulations, to modeling with differential equations.

A branch of chemistry which uses computer simulations to assist in solving chemical problems by modeling and studying chemical systems, and chemical behaviour.

It uses various methods from theoretical chemistry (from approximations of the Schrödinger equation to Monte-Carlo simulations to modeling with differential equations), incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids. It is necessary because the quantum many-body problem cannot be solved analytically, much less in closed form.

While computational results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena. It is thus widely used in the design of new drugs and materials.

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Pros and cons of Cartesian vs. Z-matrix representations of molecules?

Over the course of my studies, I have switched largely from using Z-matrix representations of molecular geometries in calculations to Cartesian representations. The software that I use now makes it easy to add the sorts of…
Richard Terrett
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Why not simulate every particle properties and interactions?

Today we have huge computational power (which is even significantly larger with supercomputers). I know that computational chemistry is used sometimes to predict particle properties. As I read on Wikipedia: Present algorithms in computational…
CatusRomus
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Why a TS must have only one negative frequency

The vibrational frequencies are related to second derivatives; a minimum will have only positive frequencies while transition state should have one negative frequency. The vibrational analysis must be performed at the the optimized geometry.…
NotEvans.
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Modern alternatives to Gaussian

Specifically, I'm curious if there are any programs which come close to Gaussian in breadth but also take advantage of things such as GPU processing. There's a page on wikipedia that goes through several options but I'd like to get feedback from…
Radu
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Gaussian: Relaxed scan with modredundant optimization and dummy atoms

I would like to perform a relaxed scan in Gaussian09 on my molecule using the modredundant optimization. Because I want to scan over two bond lengths simultaneously, I defined some dummy atoms which are close to the real atoms whose bond lenghts…
shrx
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Is it possible for the kinetic energy integral to be negative?

Is it possible for the kinetic-energy integral, Tij, to be negative? I was messing around with some HF code and found that the integral became negative on some off-diagonal terms. (This could also be a bug with the code.) If the kinetic energy…
ANZGC FlyingFalcon
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GAMESS and Gaussian : what is the maximum efficient number of supported nodes?

I have looked at GAMESS and Gaussian manuals but can not find the maximum number of efficient nodes. As I tried GAMESS on our supercomputer, I can add as many CPUs as I want but it really does not Improve the calculation time and efficacy . On the…
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Educational practice problems/systems/reactions in computational chemistry

I am not sure if this question is suitable for Chemistry SE, but I think fairly objective answers can be given, and not just I will benefit from them I have almost completed the first year of a MSc program in theoretical (and computational)…
Yoda
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Andersen thermostat in MD with rigid bond constraints

I have been writing a custom MD code for some time. I have been using the Andersen thermostat, mainly because its ease of use, and the fact that I am not concerned with gathering dynamical data, but rather free energies. I have implemented the SHAKE…
user3225087
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Is ground-state structure of a molecule entirely determined by the positions of the nuclei?

I'm a computer science with only a weak undergraduate chemistry background, but have recently become interested in simulation methods for computational chemistry. Many simulation methods, such as DFT, make the Born-Oppenheimer approximation (nuceli…
Eric J
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Cauchy-Schwarz inequality for integral derivatives

The Cauchy-Schwarz inequality for regular two electron integrals is given as: $$\left(\left.ab\right|cd\right)\leq\sqrt{\left(\left.ab\right|ab\right)}\sqrt{\left(\left.cd\right|cd\right)}$$ Now this can be differentiated with respect to…
Erik Kjellgren
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U- or RO-method for Singlet-Triplet Gap?

When I want to compare the energy between two different spin states of the same molecule, i.e. singlet-triplet-gap, do I better use unrestricted or restricted open formalism to compare the energies between both? Further on, do I need to calculate…
pH13 - Yet another Philipp
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When using Gaussian to calculate NMR, what's the default solvent and frequency?

If I choose GIAO HF/STO-3G, is the default solvent $\ce{CD3Cl}$? Is the default frequency for $\ce{^1H-NMR}$ 500 MHz? What about the frequency for $\ce{^13C-NMR}$?
OhLook
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Animate molecular vibrations as multiple xyz coordinate files

I have a frequency calculation by Gaussian09. Now I would like to extract vibrational modes as a set of xyz coordinate files. I would like to manually recompute numerically the points along a transitional vector, since IRC calculations all fail. (I…
Martin - マーチン
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Python command line tool to get chemical structure

In computational chemistry, we need to provide an starting molecular structure to start our calculations. Is there any way to get that from a chemical database? Say, I want to run H2, it would call something like …
Osman Mamun
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