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

From: Matthew Guberman-Pfeffer <>
Date: Mon, 11 Oct 2021 15:49:06 -0400

Carlos, your comment about the different temperature dependences of bimolecular interactions is very interesting. Could you comment a bit more or suggest some references? I’m trying to understand why the ionization energy for a heme group becomes more negative from 300 to 270 K, and my only idea so far has been to compute the ionization energies at the QM level for MD snapshots with various groups (non-polar, polar, acidic, etc.) electrostatically turned off. This was the context for my question about turning off H-bonds. In any case, I apologize for the interjection; your comment was just too interesting and relevant to my own work to pass up the chance for more information.


> On Oct 11, 2021, at 3:40 PM, Carlos Simmerling <> wrote:
> *Message sent from a system outside of UConn.*
> 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
> validation.
> 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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>> AMBER mailing list
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Received on Mon Oct 11 2021 - 13:00:03 PDT
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