Closed pultar closed 1 year ago
I think I can answer parts of my question:
For reaction complexes, I assume this is where energy estimated are made?
Hi – sorry for taking so long to reply – too many side projects and not enough time!
Why does the option with_complexes for the calculate_reaction_profile function produce a second maximum? I could not find any files associated with a second transition state in the folder structure.
As you found it's a effective barrier rather than a real value. It probably should be temperature and solvent dependent but probably not a huge effect. Agree that there being a number on a plot make it rather unclear – perhaps it should be ommited if estimated?
In general, do you recommend using this flag or omitting it and just have autode start from two separate xyz files, also having in mind the requirement to set the discouraged allow_association_complex_G flag?
Unless there's a possibility the potential energy difference to the association complex is strongly negative (i.e more than the ~10 kcal mol-1 entropy barrier) then you'll get an equally accurate answer with with_complexes=False
.
I was also wondering about the structures found in output: Do I understand correctly that v1yjY7_reactant.xyz would be the reactant reactive complex and v1yjY7_product.xyz the product reactive complex (before relaxation / dissociating)? It is especially unclear to me what would be the meaning of a reactive product complex if there is only one product.
You're totally right on this one. The product complex is the same as the product in this case and sadly the code isn't smart enough to omit printing it.
Maybe you could comment on the identity of each of the five transitionary points in my plot?
r0 = ethylene r1 = butadiene p = cyclohexene
r0 + r1 -> [no structure]‡ -> r0.r1 -> [TS]‡ -> p
Thank you so much! That explanation was very helpful!
First of all, thank you for providing
autode
, it really is an amazingly useful tool!I was wondering if you could comment on a couple of questions I had regarding its usage:
Why does the option
with_complexes
for thecalculate_reaction_profile
function produce a second maximum? I could not find any files associated with a second transition state in the folder structure.also suggest there is no second transition state for associating reactant A with reactant B.
So my question is, if a barrierless reaction is assumed, how come I get very specific number in my plots suggesting the presence of a second transition state?
In general, do you recommend using this flag or omitting it and just have
autode
start from two separatexyz
files, also having in mind the requirement to set the discouragedallow_association_complex_G
flag?I was also wondering about the structures found in
output
: Do I understand correctly thatv1yjY7_reactant.xyz
would be the reactant reactive complex andv1yjY7_product.xyz
the product reactive complex (before relaxation / dissociating)? It is especially unclear to me what would be the meaning of a reactive product complex if there is only one product.Maybe you could comment on the identity of each of the five transitionary points in my plot? Even after studying your paper and the documentation, I don't understand how
autode
identifies these points.To Reproduce I attached some files of the simple reaction shown here:
test-complexes.tar.gz
Environment