Re: [AMBER] elevated temperature MD

From: Carlos Simmerling <>
Date: Mon, 19 Apr 2010 13:21:57 -0400

my opinions....
it isn't clear that there is a 'temperature' when force fields are
fit. they are typically fit to minimized energies (ie 0K) and
temperature effects are entropic, relating to populations of alternate
structures at higher T. I've also seen claims of force fields being
'optimzed' to 300K and don't know why this is stated. some terms, such
as vdw parameters, are fit using liquid properties at a T, but clearly
electrostatics are not (at least in amber). of course testing may be
done at particular T, and solvent models may perform best at
particular T, but there isn't a 'temperature' in fitting.

statements such as helices being 'stabilized' are more difficult to
demonstrate than one might think from casual reading of the
literature, and are certainly model dependent and therefore the
applicability of high T MD cannot be generalized across various force
fields and protocols (NVT vs NPT, for example).

On 4/19/10, Steve Seibold <> wrote:
> Hello
> I apologize for this being a general question and not a proper "AMBER" one,
> but would sincerely appreciate any insight or short response/direction from
> the experts. I searched the literature, but I could not find a review that
> stated the consensus on these issues.
> How well are force fields adapted to higher temperatures? Are not the force
> fields generated and tested using temperatures at ~300K? I have looked in
> the literature and found that the helix structure appears to be over
> stabilized at higher temps, and so, is it safe to say that at higher
> temperatures (~400K and higher) protein simulations are more qualitative and
> exploratory than accurate in their residue contacts?
> Thank you,
> Steve
> _______________________________________________
> AMBER mailing list

Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80           Phone: (631) 632-1336   Fax: 632-1555
Stony Brook University           E-mail:
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Received on Mon Apr 19 2010 - 10:30:03 PDT
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