Re: [AMBER] Accelerated dissociation events in MD simulation by temperature increase?

From: Carlos Simmerling <>
Date: Mon, 11 Oct 2021 15:40:09 -0400

there is a long (but now mostly abandoned) history of using heating to
unfold proteins and study pathways. I'm not aware of studies that compare
dissociation pathways across temperatures. others may have more experience
and specific references for you, but I would caution that the different
interactions in biomolecules have different temperature dependence
(electrostatics, hydrophobic effect and so on). It's certainly possible
that this balance is not the same at an elevated temperature, which could
give rise to artifacts. Of course there is a long history of using
temperature to speed convergence of thermodynamic data, particularly with
reweighting approaches such as REMD. I would just be careful about using
the high-temperature data directly, or at least put more emphasis on

On Mon, Oct 11, 2021 at 3:34 PM Liao <> wrote:

> Dear Amber experts,
> If I want to speed up a ligand-protein dissociation event, I see there are
> many papers out there, but I haven’t yet found anyone using heating to do
> it. Is there a major problem that prohibits people from taking this
> approach?
> In fact one of my current projects is a lot based on heating. I’d be
> extremely glad to discuss and take feedback from anyone (off-list) who has
> experience or interest in heating analysis of protein-ligand systems.
> Thanks very much.
> —————
> James Liao
> Postdoctoral Fellow,
> UW Madison
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Received on Mon Oct 11 2021 - 13:00:03 PDT
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