Question/Issue: Index Error running BD-Milestone about seekr2 HOT 11 CLOSED

Hi Lane,
thank you very much for your help. Yes you are right, I was using an older code when preparing the input files. I am not sure if I could run the bd-milestone using the older code but I will try regenerate the input and repeat the simulations with the newer code as you suggested.

Regarding the high CPU-count. It is certainly not an efficient way of performing the simulations. I was trying to speed up the BD-part during times with low occupancy at our cluster. I see some improvement using multiple nodes (infiniband connected) however, generally it is not worth it.

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Yes it does. I was looking at different ionic radii in the literature but couldn't find the exact ones you used and wanted to make sure whether I have the correct radii.

Thank you very much again for your help, I really appreciate it!

from seekr2.

Hi Jens,

To answer your first question, you should be able to run MD or BD in any order.

So this looks like some sort of bug. Are you able to send me a tarball of the files that generate this error?

And you're welcome, I'm happy to help you get your systems running.

from seekr2.

Hi Lane,
thank you for your help. I created a tarball with the seekr-root directory and the seekr-input file. Here is a link to the tarball in my OneDrive. Please tell me if it doesn't work.

Link: https://1drv.ms/u/s!AldqnraKFN73ga04uohmv8jjoX0L7Q

from seekr2.

Thank you, Jens. I was able to download it. I'll take a look at this and get back to you as soon as I get to the bottom of the issue.

from seekr2.

Jens, would you also mind sending the equil/, apbs/ and SMD1/ directories as tarballs, just so that I can debug the seekr2 preparation scripts with your input structures?

from seekr2.

Yes of course, sorry for that.

Here:
https://1drv.ms/u/s!AldqnraKFN73ga03I_XiBrQe9qGp8w?e=9OsOzB

from seekr2.

Hi Jens,

Thanks for sending these files.

It turns out that this problem you encountered was caused because about two or three weeks ago, I made a pretty big change in how SEEKR2 handles BD simulations, and I changed quite a few things about file formats, etc. It looks like you had, by chance, downloaded and ran some simulations using the older version of SEEKR2, and when you updated and tried to run additional simulations, the files were no longer compatible with the software. If you do the following steps, you should be able to complete your simulations.

1. First, you'll need to delete the directories "b_surface" and "bd_milestone_0" and all their contents because your BD simulations will have to be redone.
2. Then, re-run the prepare.py script on your input XML file. This should keep all your MD simulations intact.

Now, you should be good to go, but I've been working on some code changes that will prevent this error in the future. But if you follow these steps they should work with the existing code. But if you want to wait until I push the latest code, you can do that too.

By the way, I noticed that you're using 496 threads for the BD stage. This seems like an unusually large number of cores to use for a shared memory process like Browndye. Are you sure that this is correct?

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Hi Jens,

You're welcome, and all that sounds good to me.

I did just push the latest version of the seekr2 code, so I'd recommend pulling and installing with "python setup.py install" before running the prepare.py and run.py scripts. Good luck.

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Hi Lane,
thank you for the update. I updated the code and restarted the simulations. I hope you will not update the code to a state which requires the MD-part to be rerun :D

Anyway, I had another question unrelated to this issue. But I was wondering how you were choosing the ion-radii for the BD-simulations?
I have seen you were citing a paper for the radii of TRIS in the original SEEKR publication but I was not able to understand how you calculated these.

Publication:
Schindler, P.; Robinson, R. A.; Bates, R. G. Solubility of Tris(Hydroxymethyl)Aminomethane in Water-Methanol Solvent Mixtures and Medium Effects in Dissociation of Protonated Base. J. Res. Natl. Bur. Stand., Sect. A 1968, 72A (2), 141−148.

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Hey Jens,

Yes, the ion radii for the BD simulations are used to determine the solvent accessibility, particularly in the APBS calculations. In the past, we had been using radii from example APBS input files, and also from publications, when radii or diffusion coefficients were available (as in the case of Tris, as you mentioned). As time has gone on, I have realized that the best radii would probably come from Born radii (since they represent solvent accessibility), particularly the mbondi2 set, since we typically use those to make the PQR files. In fact, probably the best way to get those radii is straight from a PQR file after running "ambpdb" on the prmtop and inpcrd files.

Does that answer your question?

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