[gmx-users] How to set the temperatures for REMD?

[Alessandra Villa]

Hi,


On Wed, Jan 22, 2020 at 5:55 PM ZHANG Cheng <272699575 at qq.com> wrote:

> My purpose of running REMD is to generate sufficient conformation
> sampling, and try to use them to explain the in vitro data at 65C (338.15K).
>
>
> I am using the "Temperature generator for REMD-simulations" at
> http://folding.bmc.uu.se/remd/
>
>
> I am not sure about the "standard/default" values of several parameters.
> Can I ask how to determine them?
>
>
> 1) Exchange probability: it should be a value between 0 to 1. The higher
> of the value I set, the shorter intervals of the temperatures are
> output.&nbsp;
>
>
>
For the definition of exchange probability (isobaric and isothermal
ensemble) between 2 replicas i and j see eq 4 in
http://manual.gromacs.org/documentation/2019-current/reference-manual/algorithms/replica-exchange.html?highlight=replica%20exchange

Best regards
Alessandra


> 2) Tolerance: by default it is 1e-4. So I just use it?
>
>
> 3) Lower/Upper temperature limit: As I am interested in 338.15K, should
> the lower limit set to be 338.15K, while the upper limit as 373.15K
> (i.e.100C)? Should it be even higher?
>
>
> 4) Constraints in water: Fully flexible?
>
>
> 5) Constraints in the protein: All bonds?
>
>
> 6) Hydrogens in protein: All H? (what does this mean?)
>
>
> Is there a general rule for the number of temperatures used in the REMD?
> Please feel free to tell me if there is a guidelines for setting the
> temperatures.
>
>
> Thank you!
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