[gmx-users] [gmx-user] 300K vs 310K for molecular dynamic simulation

[Myunggi Yi]

Dear Quin,

Since the lab temperature is around 300K, people who want to reproduce some
specific (in vitro) experiment results run simulation at 300K.
What is your target? Experimental condition? body temperature?

It's up to you.

If your simulations show significantly different results by 10K difference,
then it's very interesting.
If you have enough sampling, then it's interesting.
However, if your sampling is not enough, then you need to run MD longer
and/or more.
Carefully analyze them and publish your results.

Best wishes,


On Sat, Dec 28, 2019 at 10:10 PM Quin K <profiles.ke at gmail.com> wrote:

> Hi
>
> Which temperature should be used for molecular dynamic simulation of a
> human protein?
> If we used 300K would that give significantly different results from 310K
> MD simulation?
> Some argue that since human body temperature is around ~310K MD should be
> done at 310K.
> However I saw many papers that have used 300K for MD of human proteins.
>
> Thanks
> Regards.
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