Replies: 8 comments
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I can answer these questions, and I've also made some changes to the development version of MOPAC in response to them (that will appear in the next MOPAC release).
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Please keep the PM8 model in the code - I'm using it for my parametrization experiments and it will turn into a real PM8 in the future. Keeping it in the code would make it easier to sync my development branch with the main version. |
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@ggoetten > Lastly, I would like to know which kind of compounds THERMO should be used for For a nice handle on this problem in general, you should looks at Grimme's work with their mRRHO method, |
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The relevant reference for CREST's anharmonic corrections appears to be [https://doi.org/10.1039/D1SC00621E]. It uses a model that regularizes the free-energy divergences from low-frequency modes by approximating them as coming from rigid rotors, which is probably a good approximation for the rotations of small sp3-bonded side groups as in the original post. A path to interfacing between MOPAC and CREST would certainly be welcome. I'm planning to add a directory in the MOPAC repo for pre/post-processing scripts, and I've received a few contributions this year over email. This script might fit in there. |
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@godotalgorithm > a good approximation for the rotations of small sp3-bonded side groups as in the original post. In fact mRRHO seems to handle much more, e.g. non-covalently bound complexes, as well. Indeed Grimme has a lot of earlier published work on it. The nice thing about CREST is that its THERMO module can be used as stand-alone processor for externally provided vibrational frequencies (so one needs not re-implement the algo in MOPAC, although that would be nice too). Regarding the script directory, having a dedicated place for collecting them is an excellent idea. I am too lazy/busy to learn something modern like Python for this, alas ;-), so my code is quaint in awk. |
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I do have an interface to MOPAC in my Cuby framework (
http://cuby4.molecular.cz/) where the rotor approximation can be applied
(using the keyword 'thermo_low_mode_fix'). At the moment, this may be the
most straightforward access to this combination of methods.
…On Wed, Jul 12, 2023 at 9:25 PM Zoli Fekete ***@***.***> wrote:
@godotalgorithm <https://github.com/godotalgorithm> > a good
approximation for the rotations of small sp3-bonded side groups as in the
original post.
In fact mRRHO seems to handle much more, *e.g.* non-covalently bound
complexes, as well. Indeed Grimme has a lot of earlier published work on
it. The nice thing about CREST is that its THERMO module can be used as
stand-alone processor for externally provided vibrational frequencies (so
one need not re-implement the algo in MOPAC, although that would be nice
too).
Regarding the script directory, having a dedicated place for collecting
them is an excellent idea. I am too lazy/busy to learn something modern
like Python for this, alas ;-), so my code is quaint in awk.
But it works for me.
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Cool! I've been tempted to try Cuby for quite some time, maybe this will push me over the edge to actually do it ;-)... |
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This Issue has been moved to a Discussion because it was resolved by clarifying existing features and did not constitute a bug report or new feature request. |
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Hello,
I have a couple of questions that I would love some answers.
First I would like to know if there is any information on precision of PM8, as it has been done to PM7 on the mopac website.
The second is that I am trying to run a polymer to calculate the vibration, but it says "Insufficient memory to run FORCE", I have 16 gb of Ram which is probably not much, and I am even using MOZYME recommended by the package. I guess there is nothing to be done correct? I even used FORCETS. It is very interesting that the energy minimization runs quite fine using PM7, RM1...
Lastly, I would like to know which kind of compounds THERMO should be used for, I tried to run some common drugs and none fits the criteria (paracetamol or caffeine). The system is only increasing as a straight line ? I don't know if it is my lack of background on physics but that doesn't fit the experimental data on Cp. No error is reported to the log file as well by mopac.
MOPAC executable
Operating system
Additional context
Add any other context about the problem here. (e.g. Linux distribution if that might be relevant)
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