[gmx-users] atom moved too far

[Justin Lemkul]

On 1/2/20 3:02 PM, Christos Deligkaris wrote:
> thank you Justin.
>
> I saw on your umbrella sampling tutorial how to implement the restraints
> using the pull code.
>
> The protocol I used is (if I understand correctly your question): The
> energy minimization reached the cutoff for maximum force 1000 in 346 steps.
> My NVT equilibration was 50,000 steps of dt = 0.002 and I used 8 NPT
> equilibration calculations, each with 31,250 steps of dt=0.002 (total NPT
> equilibration time 500ps) where I slowly decreased the position restraints
> on DNA and the small molecule, as well as the harmonic restraint between
> the two.
> What are the best temperature coupling groups to use when we are not
> certain whether the small molecule will spend the entire simulation period
> physically bound to the macromolecule or whether it will become fully
> solvated at some point? Is Macromolecule and Non-macromolecule the best
> option since the small molecule will always (to a small or large extent)
> interact with water (versus the Macromolecule_and_small_molecule and
> everything else grouping option)?

I doubt there would be a measurable or provable difference between the 
behaviors of the two setups.

-Justin

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Justin A. Lemkul, Ph.D.
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