Hi Matthew,
On Fri, May 12, 2023 at 9:56 PM Matthew Guberman-Pfeffer via AMBER <
amber.ambermd.org> wrote:
> Dear AMBER community,
>
> Can force fields be trusted
No
...Jokes aside, unless someone else chimes in with more knowledge, it is
probably fair to say that your use case has not been thoroughly tested
before. Unless there is a trustworthy study you are trying to replicate
here, be prepared to validate the accuracy of your model yourself. As you
suggest, I think there is sufficient literature on pulling simulations to
claim that MD simulations do describe mechanical deformations of proteins
in a reasonable fashion, broadly speaking. Does that mean simulations (and
precisely what kinds of simulations) will be useful for the specific
question you are trying to answer is probably a lot less clear. Maybe there
is some kind of experimentally well characterised simplemost change you
could simulate as validation, e.g. some protein that undergoes a
conformational change under pressure?
Kind Regards,
Thomas
> to simulate elevated pressure-induced conformational effects?
>
> I’ve seen this done for pulling simulations, but what I have in mind here
> is to simulate the effects of compressing a protein between two surfaces
> (molecular junctions). Does this seem like a valid use of MD?
>
> Best,
> Matthew
>
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--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Mon May 15 2023 - 00:30:02 PDT
