Yes in explicit solvent this can be much smaller (like 10).
On Thu, Jul 20, 2023, 1:07 PM Yang, Li-Yen via AMBER <amber.ambermd.org>
wrote:
> Hello,
>
> I am trying to run a pH constant simulation with explicit solvent.
>
> In the manual, under the section 26.3.1. Running at constant pH in
> implicit solvent, it is mentioned:
> “Constant pH MD techniques employ a reference (model) compound to compute
> relative free energy differences between the various protonation states
> through a thermodynamic cycle … In order to obtain sensible results, you
> must run your simulations with the same potential energy function for your
> system that was used to derive these reference energies. The reference
> energies were derived using the following parameters:
> cut=30.0, ….”
>
> My question is, does this also apply to constant pH in explicit solvent?
> The reason I am asking is that I tried using a cutoff of 30, but the
> simulation is pretty slow (takes over a month to run a complex with around
> 5500 atoms).
> I was wondering if it is ok to set it to a smaller value?
>
> Thank you!
>
> Best,
> Zoey
>
>
>
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Received on Thu Jul 20 2023 - 11:30:02 PDT
