Help: Suggestion for gaussian calculation setup involving nanoparticles and DNA

sobereva

rpestana94 发表于 2021-3-30 21:58
Prof Sob another question, make sense to optimize the nanoparticle by it self and the optimize aga ...

If there is no special reason, just optimize the complex.

rpestana94

sobereva 发表于 2021-3-30 12:58
If there is no special reason, just optimize the complex.

thanks

rpestana94

sobereva 发表于 2020-11-26 22:08
You can use VMD program to dig out a spherical cluster from supercell of metal

Prof Sob, i have a question about the construction of the nanoparticle, I'm trying to use charmm-gui to build it but I get an odd number of gold atoms, this gives problem with orca calculation due to the multiplicity, so how I can solve this multiplicity problem or better try to get one nanoparticle with even number of gold atoms?

sobereva

rpestana94 发表于 2021-4-6 23:43
Prof Sob, i have a question about the construction of the nanoparticle, I'm trying to use charmm-g ...

Use GaussView to properly edit your nanoparticle (e.g. delete an atom or add a atom)

rpestana94

sobereva 发表于 2021-4-6 11:31
Use GaussView to properly edit your nanoparticle (e.g. delete an atom or add a atom)

if I remove or add one atom it can be randomly or for example I should remove the center one, the interaction with this will be really low or zero but not sure if this can destabilize the whole structure or better remove one on the surface?

sobereva

rpestana94 发表于 2021-4-7 01:05
if I remove or add one atom it can be randomly or for example I should remove the center one, the  ...

I can't give you answer because I know nothing about character of your practical system.

rpestana94

sobereva 发表于 2021-4-6 12:20
I can't give you answer because I know nothing about character of your practical system.

Thanks for the advice I solve the problem

rpestana94

sobereva 发表于 2021-3-29 23:52
Your keywords are incorrect.

If your nanoparticle is very large, due to consideration of comput ...

Professor Sob thanks for this recommendation for this basis set in gaussian16 how it would be? Here I will try to guess the correct keywords but let me know if I'm wrong:

For opt
opt pbepbe/3-21+g/def2sv geom=connectivity

For single point
pbepbe/3-21+g/def2tzv geom=connectivity

I don't know if the dispersion correction is already added by default in gaussian

Thanks in advance

zjxitcc

rpestana94 发表于 2021-6-25 11:20
Professor Sob thanks for this recommendation for this basis set in gaussian16 how it would be? Her ...

These keywords will not provide any meaningful result.

For practical computation, a double-zeta basis set is at least required, such as def2SVP, 6-31G(d,p), 6-31G(d), etc. So 3-21+g is useless.

For RI (or density fitting), you should use ORCA instead of Gaussian, since density fitting in Gaussian does not accelerate the computation (or acceleration is little). But this is significant in ORCA.

rpestana94

zjxitcc 发表于 2021-6-24 22:29
These keywords will not provide any meaningful result.

For practical computation, a double-zeta ...

orca is significantly faster than gaussian for general purposes or just with the dispersion?

zjxitcc

rpestana94 发表于 2021-6-25 11:36
orca is significantly faster than gaussian for general purposes or just with the dispersion?

ORCA is much faster than Gaussian for RI (or density fitting) related computations. If RI is turned off, ORCA may be slower than Gaussian (but it also depends on which method you use).

By the way, the dispersion correction keyword in Gaussian is em=GD3 or em=GD3BJ, where 'BJ' means with Becke-Johnson damping. The dispersion correction is not default, and you should add it explicitly. You can find this on http://gaussian.com/dft. Dispersion correction costs little time (less than 1s, or only several seconds) in any quantum chemistry software.

rpestana94

zjxitcc 发表于 2021-6-24 22:43
ORCA is much faster than Gaussian for RI (or density fitting) related computations. If RI is turne ...

Thanks

sobereva

rpestana94 发表于 2021-6-25 11:36
orca is significantly faster than gaussian for general purposes or just with the dispersion?

ORCA is significantly faster than Gaussian for single point and optimization tasks when RIJ (for pure DFT functionals) or RIJCOSX/RIJK (for hybrid DFT functionals) or RI (MP2 and double-hybrid functionals) is enabled for medium and large-sized systems.

However, speed of frequency analysis of current version of ORCA (4.2.1) doesn't outperform Gaussian even if RI related techniques is enabled.

Gaussian also has RIJ for pure DFT functionals, however it significantly speeds up calculation only when you use relatively large basis sets (e.g. def2-TZVP) or in frequency analysis process.

Overall, you can benefit from RI related techniques in ORCA much more than Gaussian.

wzkchem5

sobereva 发表于 2021-6-25 11:09
ORCA is significantly faster than Gaussian for single point and optimization tasks when RIJ (for p ...

As a side note: ORCA 5.0 will be released on next Thursday. The frequency calculation of ORCA 5.0 will be noticeably faster than in ORCA 4.2.1. But due to some (in)famous reasons I cannot comment on whether ORCA 5.0 will become faster than Gaussian in this aspect.

rpestana94

sobereva 发表于 2021-6-25 05:09
ORCA is significantly faster than Gaussian for single point and optimization tasks when RIJ (for p ...

Three questions, about the basis sets in gaussian how it would be? I have your recommendation in ORCA but I don't know exactly how to translate this to gaussian, is there a way to do this automatically?

If I'm right gaussian16 have some GPU acelleration for some process, ORCA have something like this?

The RIJCOSX and this kind of keywords actually accelerate the calculation but I understand that this also give some error in the measurement, It will be better to do a calculation with RIJCOSX activate and then a new calculation deactivating RIJCOSX or the error is too low