Re: [AMBER] scientific issue

From: Alexander Izvorski <>
Date: Sun, 26 Dec 2021 13:29:53 -0800

Second what David said - probably the kinetics are key. A simple example
of exactly what you're describing would be lipids in water - of course the
lipids would aggregate (into droplets, micelles etc). Now add some
detergent - indeed the detergent would initially aggregate with the lipid
droplets as well :) it may take a long time (maybe even microseconds) to
see any droplets spontaneously breaking up.

Some things to think about: what do the aggregates look like? In a lot of
cases they would have a specific structure (crystal, filament, micelle
etc). What does the "dispersed aggregate" look like? (smaller aggregates
capped with the second molecule, etc) What is the transition pathway? You
may have an easier time simulating (or observing) single steps along the
transition pathway rather than looking for (eg) spontaneous disaggregation
of large aggregates.

On Wed, Nov 10, 2021 at 8:05 AM David A Case <> wrote:

> On Wed, Nov 10, 2021, SOMA ROY wrote:
> >
> >Problem: I am simulating the aggregation of some small molecules (small
> >molecule-1). After the simulation, I am going to add another small
> >molecule (small molecules-2) to the nanoaggregates which may dissipate the
> >nanoaggregates as observed from the experimental data. Now, I have
> >performed the simulation of the small molecule-1 aggregation. When I have
> >added the small molecule-2 to the aggregates, it is clumping with the
> small
> >molecule-1. How should I simulate the dissipation of the small molecule-1
> >nanoaggregates after the addition of the small molecule-2?
> This might be a kinetic problem, that is takes a long time for molecule-2
> to
> dissipate the aggregates. It may also be a force-field problem: the system
> may favor nanoaggregates even when molecule-2 is present. Or, the
> experimental setup and that in the simulation may be different; are you
> sure
> your simulated concentrations are realistic?
> One thought: try starting with both molecule-1 and molecule-2 as monomers,
> and see if there is a difference in aggregation compared to the simulation
> where no molecule-2 molecules were present.
> This is a very complex problem, and it may take a lot of work to create a
> physically-realistic simulation. Don't lose sight of the fact that you
> want to learn something new from the simulations, and not just reproduce
> known experimental results. Even "failed" simulations may lead to novel
> insights.
> ...dac
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Received on Sun Dec 26 2021 - 14:00:02 PST
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