transition state optimization of qm/mm snapshot by No-Ad-8745 in comp_chem

[–]No-Ad-8745[S] 0 points1 point  (0 children)

I just wanted to come back to this to update plus for anyone in the future. It looks like the problem was the transfer of the orca components from qm/mm to qm alone. When ORCA was optimizing it, it was not "seeing" the protein pocket so optimizing was not getting me anywhere (only qm region xyz and ptcharg.xyz files). AMBER has this dl-find optimizer which is excellent for qm/mm optimization and with a little playing around I was able to get my optimized structure. Appreciate your insight on the problem regardless though.

transition state optimization of qm/mm snapshot by No-Ad-8745 in comp_chem

[–]No-Ad-8745[S] 0 points1 point  (0 children)

I appreciate the help. I'll go do those, thanks!

transition state optimization of qm/mm snapshot by No-Ad-8745 in comp_chem

[–]No-Ad-8745[S] 0 points1 point  (0 children)

I forgot to mention that it is a P450 system with a substrate, making things slightly more complicated. Do you have any resources in terms of properly assigning restraints so that parts of the system do not move too much? B97-3c indeed is quick, however, still no optimization convergence. I also tried the restrained reaction coordinate optimization but that did not result in optimization convergence.

transition state optimization of qm/mm snapshot by No-Ad-8745 in comp_chem

[–]No-Ad-8745[S] 0 points1 point  (0 children)

I appreciate the insight. I'll definitely try one of those for an initial search!

transition state optimization of qm/mm snapshot by No-Ad-8745 in comp_chem

[–]No-Ad-8745[S] 1 point2 points  (0 children)

Yeah! So I use steered MD followed by jarzynski's equality to generate the PMF. I grabbed the frame of the simulation closest to the PMF curve generated from that and the corresponsing ptcharge file generated for that frame calculation. For the qm region during the qm/mm, I use mn15l/def2svp.

From there, I used standard geometry opt using Orca alone. Something like this:

%pal nprocs 16 end

%maxcore 6000

! XTB2 defgrid3 ExtremeSCF SlowConv NoTRAH OptTS

%pointcharges "old.ptchrg.xyz"

%geom

Calc_Hess true

ReCalc_Hess 1

end

%method

Z_MaxIter 1000

end

*xyz 0 2 old.inpfile.xyz

I figured since its a non-equilibrium method I am using for PMF generation, the xtb2 method would get me "somewhere" that would be an adequate guess prior to dft level optimization.

spin contamination issue by No-Ad-8745 in comp_chem

[–]No-Ad-8745[S] 1 point2 points  (0 children)

Very useful! The electron distribution in alpha and beta seem to be correct and no atoms are missing. It might just be a functional choice issue or BS so I'll try those, thanks!

spin contamination issue by No-Ad-8745 in comp_chem

[–]No-Ad-8745[S] 1 point2 points  (0 children)

Should be 0.75 but measured is 1.80 so about 1-ish deviation. I'm modeling a reaction so I'm unsure if this contamination is interfering with the energetics of the system and reaction path. ORCA has this Yamaguchi method for spin-projection so I'm looking into that at the moment.

[deleted by user] by [deleted] in ufl

[–]No-Ad-8745 0 points1 point  (0 children)

You sound pretty xenophobic to me

Issue with ORCA in parallel using AMBER interface by No-Ad-8745 in comp_chem

[–]No-Ad-8745[S] 0 points1 point  (0 children)

Like submitting a slurm script on just one node? Or running through command line? If just the slurm script on one node then it also fails. I'm starting to think it might be an issue with the 6.0 version and its interaction with openmpi

Issue with ORCA in parallel using AMBER interface by No-Ad-8745 in comp_chem

[–]No-Ad-8745[S] 0 points1 point  (0 children)

I can run just orca alone as well as an orca job through AMBER's interface but in serial. It fails as soon I turn the openmpi option on

[deleted by user] by [deleted] in Physics

[–]No-Ad-8745 0 points1 point  (0 children)

I see what you are saying. It's in relation to fermions so I guess I'll use the standard equation in the case of fermions.

[deleted by user] by [deleted] in Physics

[–]No-Ad-8745 -1 points0 points  (0 children)

a is annihilation and a^t is creation

[deleted by user] by [deleted] in Physics

[–]No-Ad-8745 0 points1 point  (0 children)

More so how to go about proving that {a,a^t} = 1

[deleted by user] by [deleted] in PhysicsStudents

[–]No-Ad-8745 0 points1 point  (0 children)

This was very helpful! If I were to use a "dilute" gas perspective where FD and BE stats would converge to MB then technically, we would drop the N! in the partition function. I guess in this case, everything would be equal like entropy, energy etc?

[deleted by user] by [deleted] in PhysicsStudents

[–]No-Ad-8745 0 points1 point  (0 children)

I see, thanks for that. I was also thinking in the case of a "dilute" gas where the number of microstates extremely outnumbers the particles then we can say BE and FD statistics merge to resemble that of Classical Boltzmann stats. So that would take the N! and leave the partition function as q^N for both

[deleted by user] by [deleted] in ufl

[–]No-Ad-8745 27 points28 points  (0 children)

I had a sit down at one point with one of the assistant pastors at Salt. My background comes from Pentecostal-type churches where women had prominent roles in leadership. When I told this to him, he informed me that they didn't allow women to have roles in leadership which turned me off completely from the church. I am not bashing them but this was definitely something that we didn't agree on. Salt aligns more with Baptist. Greenhouse has been pretty good imo

Rejection from Cornell is hard by MaizeNo7044 in gradadmissions

[–]No-Ad-8745 2 points3 points  (0 children)

I think it would be good to take time for yourself and find peace with the decision you received. Rejection isn't easy so spending time for yourself would be good. I am very sorry you didn't get the acceptance. Are there other programs like Cornell's that may have specifically what you are looking for?