Hi Christina and David,
Thanks for your comments and information. To clarify, I don't disagree that these things can and would interact in real life and that it is okay to see them interacting in a simulation. The problem was that after a relatively short amount of production MD (10s of ns), several ions would end up "stuck" (so not diffusively swapping in and out) to the ligands phosphate groups (over several 100s of ns at least), which does seem like an artefact. I have ran repeats and observed the same behaviour.
Based on what you've said Christina I'll look into the phosphate group parameters I'm using for the ligand tto make sure they aren't responsible and might also try using potassium instead given the PMFs in Figure 3 in the paper you linked.
And thank you David for the confirmation that the harmonic restraints wont work for this sort of problem, that's good to know.
All the best,
Rory
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: 25 April 2023 22:49:51
To: Rory Crean; AMBER Mailing List
Subject: Re: [AMBER] Restraining Counterions in Regular MD Simulations
On Tue, Apr 25, 2023, Rory Crean via AMBER wrote:
>
>I've therefore been working on trying to place harmonic restraints to
>prevent the sodium ions from coming too close to the phosphate groups.
First, I agree with Christina here: is this what you really want to do? How
will you avoid overemphasizing phosphate-repulsions? And, how could you
justify any quantitative results you find with such ad hoc modeling?
Second, the "NMR" distance restraints are not set up for periodicity. The
distance between a given sodium and a given phosphate may not represent the
closest distance between that Na and all of the image phosphates in other
unit cells, especially given the high mobility of ions.
So, I don't immediately see any way in Amber to achieve your goal. Maybe
others on the list have ideas.
....dac
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Received on Wed Apr 26 2023 - 01:30:01 PDT
