[gmx-users] System volume "jumps" on exact continuations

[Elizabeth Ploetz]

However, if most runs are group scheme, a quick check could show whether

jumps are present in runs that i) do PP-PME tuning ii) if logs go truncated
during continuation at least whether they do use separate PME ranks
(because otherwise CPU-only runs don't tune).

i) If grepping "timed" from the LOG file does not give any output, does that mean there was no PP-PME tuning? (Sorry for the stupid question. I'm not sure which piece of information from the LOG file is going to answer whether or not there was PP-PME tuning.) If so, perhaps there is a correlation between having PP-PME tuning and having a jump. Please see this link<http://i1243.photobucket.com/albums/gg545/ploetz/volumeJumps_zps8hmlghtn.png>. *If* the volume for 40-60ns of row 3 is the correct system volume, then all the data in this figure is consistent with there being a jump when there is PP-PME tuning. (Please note that while the data at 1 bar looks okay in this case, and elevated pressures do not, this is not always true. We get jumps at 1 bar as well sometimes.)
ii) These are all CPU-only runs. The simulations always use separate PME ranks.
Please let me know if any particular data from the LOG file would be helpful.

If I understood correctly, it's only group scheme runs where this has been
observed, so it could be some newer feature/change that interacts badly
with the group scheme.

You are correct, so far we have not seen any jumps with Verlet.

BTW, do you have any data with 4.5?

I have a few old simulations with version 4.5.3 (none with 4.5, sorry). They were all ran with inexact continuations (i.e., I did not provide checkpoint files when running multiple short runs to create one long simulation) or single trajectories that I had killed at various points and then continued using checkpoint files and -append. I don't have a huge data set with 4.5.3, but none of them exhibited jumps!

I'd suggest that (especially if if investigation of current data does not
reveal the reasons) pick a setup where you seemed to get the anomaly and
run with the same settings using the Verlet scheme lots of short runs with
restarts in a loop.

Thanks, we are doing this test.