Week n+4¶
Monday 26/7¶
What I did today:¶
- After my meeting with Katya there’s a few things I need to do:
- Generate MESPs for the efield perturbations
- Potentially redo the relaxed efield perturbations with a more appropriate integration grid for M06-2X
- Redo all the benchmarks in Psi4, since ORCA isn’t behaving nicely
- We’ve decided to not use DCA as an anion, which makes my job slightly easier
- I generated the MESPs and put them into the PyMOL project
- I tweaked the script builder job
- I submitted the better scan jobs which are doing their thing
- I might actually cancel and resubmit these with MESP generation…
- ^this has been done
- I spent a fair amount of time trying to figure out how to extract a clustered trajectory from the dcd files with mda, but I think it’s probably not the best method.
I’ve set off my MD generator script and it is now building and queueing jobs!- I’ve suspended these jobs, only because when the IL test jobs finish tomorrow, I want to be able to get them straight back on.
Tuesday 27/7¶
What I did today:¶
- All the test runs timed out as expected, so I restarted them, making sure to specify to use P100 gpus so they should finish within 24 hours.
- Submitted all the jobs I generated yesterday
- Worked on finding decent cavities for PCMSolver, which meant troubleshooting compiling geomview, before I learned that nothing else can read
.offfiles… except for https://3dviewer.net
- I settled on using a cavity area of 0.9
- Tweaked the benchmark jobs and brushed up on SCF algorithms to try and speed them up/prevent them from oscillating.
- I settled on using SOSCF, but we shall see how effective that is… (It works for ORCA)
- Mostly spent a lot of time troubleshooting XQuartz again, and also jupyterlab…
- I noticed that the temperatures of the jobs is closer to 200-230K when I’m specifying 343K for the thermostat, trying to follow up on this with Tom or Michael, but it’s late.
- This is because the reported temperature is the average of the temperature of all the particles, which Drudes have their own thermostat that keeps them at ~2K
Wednesday 28/7¶
To do:¶
- RDFs of ILs
- Load all geometry into PyMOL
- Update running jobs
What I did today:¶
- I wrote a script to load all the geometries into PyMOL in different states to make it easier to browse their respective geometries
- This should easily be extended to loading in ESPs
- I wrote an RDF generation script that uses MDAnalysis, which is much faster than TRAVIS
- I had a collaborator meeting in which Michelle was really happy with the work I’ve done and wants to get it into a paper, but now I’m feeling overwhelmed
- So I just sent an email to Katya about feeling overwhelmed
- The IL pMD jobs have begun to run at speeds of ~50-55ns/day, which should mean they’ll take just over two days to complete which is reasonable
- I managed to get MDAnalysis cluster selection and exporting working! and I managed to speed up the
.dcdto.pdbconversion process, and I managed to get the geometry to read properly in pymol - The RDFs I’m getting form MDAnalysis don’t feel quite right, so I’m trying again with TRAVIS to see if looks any different.
- This didn’t but I realised the error. I was computing all atoms of one molecule against thee other, as opposed ot sat the N-S distance.
- I also used mdtraj as per Tom’s suggestion which made this process so much faster!
- Using both of these things, I’m still not seeing any difference between the two IL test jobs, but I think it might have something to do with the constant acceleration. If I compare that RDF to one of the in progress na1* jobs, I do see a difference!
-
I also forgot that I need to do comparative MD between field off and on, so I’ve queued up those jobs as well!
- I might also get them queued on M3 just in case they get picked up there sooner… - done
- I also noticed that my MonARCH jobs weren’t submitted under partner, so I’ve fixed that up
From meeting with Michelle
For a paper! (Special edition of PCCP?)
Based on analysis, we want an e-field pointing this way…
When we do, we get a rate increase of X resulting in kinetics of Y
What will give the best selectivity between the two?… (biggest ΞE)
If we only want R?… (biggest S barrier)
If we only want S?… (biggest R barrier)
Then Michelle can demonstrate how to get this through functionality
Then Joseph can test this experimentally
this can then be explored thorugh a Hammett study to detemrine the effectiveness of the susbtituent
To turn this into a paper then we need to do this for a few derivatives
Then do this in multiple solvents to demonstrate that polar solvents prevent this and that non-polar solvents help this and there’s a midpoint between the two of solubility and effectiveness
Use the Check JOC paper that Michelle just did on the Aldol reaction as a guide
Thursday/Friday¶
What I did today:¶
- I did do things… I just haven’t been feeling the best.
- I worked on pymol scripts and analysis of the efield scans mostly
Benchmark Matrix¶
| Job | na1r - r | na1t - r | na1p - r | na1r - s | na1t - s | na1p - s |
|---|---|---|---|---|---|---|
| Non-catalysed benchmark | queued | queued | queued | queued | queued | queued |
| R benchmark (static) | queued | queued | queued | queued | queued | queued |
| S benchmark (static) | queued | queued | queued | queued | queued | queued |
| Catalysed benchmark (relaxed) | ||||||
| R benchmark (relaxed) | ||||||
| S benchmark (relaxed) |
MD Run Matrix¶
| IL | na1r-r | na1t-1-r | na1t-2-r | na1t-3-r | na1p-r | na1r-s | na1t-1-s | na1t-2-s | na1t-3-s | na1p-s |
|---|---|---|---|---|---|---|---|---|---|---|
| \(\il{C4mpyr}{OTF} - \vec F =0.1\:V\cdot\AA^{-1}\)ββββ | running | queued | queued | queued | queued | running | queued | queued | queued | running |
| \(\il{C4mpyr}{MSO4} - \vec F =0.1\:V\cdot\AA^{-1}\)βββ | done | running | running | running | done | done | failed | running | running | done |
| \(\il{C4mpyr}{TCM} - \vec F =0.1\:V\cdot\AA^{-1}\)ββ | done | failed | done | done | done | failed | done | done | failed | done |
| \(\il{C4mpyr}{OTF} - \vec F =0.0\:V\cdot\AA^{-1}\)βββ | queued | queued | queued | queued | queued | queued | queued | queued | queued | queued |
| \(\il{C4mpyr}{MSO4} - \vec F =0.0\:V\cdot\AA^{-1}\)βββ | queued | queued | queued | queued | queued | queued | queued | queued | queued | queued |
| \(\il{C4mpyr}{TCM} - \vec F =0.0\:V\cdot\AA^{-1}\)ββ | queued | queued | queued | queued | queued | queued | queued | queued | queued | queued |