From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Tue Oct 20 2020 - 15:33:10 CDT
Hi Giacomo,
I really appreciate your help and the comprehensive explanation. Just to
review the details of my well-tempered metadynamics simulation, in my case
the initial hill weight is 0.1 kcal/mol and due to the limited wall time I
can't perform one long-time continuous simulation. Then I divided one
long simulation into several dependent/discontinuous short jobs each taking
one nanosecond.
I expected the hill weight to get updated when restarting dependent
simulations, but although the collective variable (CV) values are updated
properly, the hill weights are not. If I understood correctly, you meant
that since the newly added Gaussians are scaled based on the number of
Gaussians already added at the CV location, then starting the next
nanosecond of the simulation again with the starting hill weight of 0.1
kcal/mol doesn't matter, since if the CV is located at the place where
already enough Gaussians are added (depending on shape of the free energy
surface) then the hill weight would reduce automatically. I may be wrong,
but if the length of each discontinuous/dependent simulation wasn't long
enough, then the hill weight may not have enough time to reduce efficiently
before the next job starts and this causes the simulation never converges.
I did a test: I performed two simulations with the same time length of
30ns, one long continuous simulation and the other to be performed through
30 discontinuous/dependent simulations each 1 ns time-length. I put the
links for the plot of hill weight vs time for both cases, in the following.
It seems the continuous one is doing much better than the
discontinuous one. The hills over the discontinuous simulation are going up
and down periodically and it is due to the fact that the hill weights do
not update properly. I don't know how to update the hill weights over the
dependent simulations..
links:
Continuous simulation:
https://drive.google.com/file/d/1KccEAXH9sd5mtTNzOCLingNqghSqJHcW/view?usp=sharing
Dis-continuous simulation:
https://drive.google.com/file/d/1cHDM6VJrSnTHeuiy2J7tzQ9tO-6JF3Ht/view?usp=sharing
All the best,
Zeynab
On Tue, Oct 20, 2020 at 4:12 PM zeynab hosseini <hosseinizeynab93_at_gmail.com>
wrote:
> Hi Giacomo,
>
> I really appreciate your help and the comprehensive explanation. Just to
> review the details of my well-tempered metadynamics simulation, in my case
> the initial hill weight is 0.1 kcal/mol and due to the limited wall time I
> can't perform one long-time continuous simulation. Then I divided one
> long simulation into several dependent/discontinuous short jobs each taking
> one nanosecond.
>
> I expected the hill weight to get updated when restarting dependent
> simulations, but although the collective variable (CV) values are updated
> properly, the hill weights are not. If I understood correctly, you meant
> that since the newly added Gaussians are scaled based on the number of
> Gaussians already added at the CV location, then starting the next
> nanosecond of the simulation again with the starting hill weight of 0.1
> kcal/mol doesn't matter, since if the CV is located at the place where
> already enough Gaussians are added (depending on shape of the free energy
> surface) then the hill weight would reduce automatically. I may be wrong,
> but if the length of each discontinuous/dependent simulation wasn't long
> enough, then the hill weight may not have enough time to reduce efficiently
> before the next job starts and this causes the simulation never converges--00000000000087ffb605b220315a--
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