Re: [AMBER] scientific issue

From: David A Case <>
Date: Wed, 10 Nov 2021 11:04:48 -0500

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


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Received on Wed Nov 10 2021 - 08:30:02 PST
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