You may want to look at this paper for convergence issues in US:
https://chemrxiv.org/engage/chemrxiv/article-details/6567208629a13c4d4741e783
On Thu, Jul 18, 2024 at 1:47 PM Liyanage, Risi (MU-Student) via AMBER <
amber.ambermd.org> wrote:
> Dear all,
>
> I am new to running umbrella sampling simulations. I am trying to build
> the free energy profile for a base unstacking of a helix using umbrella
> sampling. I am using a 15 windows system with RC going from 4.0 to 7.75
> Angstroms. I am expecting to see a state change at around 5.0 to 5.5
> Angstroms. I am feeding the restart file of the previous window as the
> initial structure for the next window.
> My questions are,
>
> *
> Do I need to minimize, heat and equilibrate the system at the start of
> each window even if I am using the restart file from the previous window?
> *
> How does the frequency of dumping RC data to the dumpave file affect the
> free energy profile?
>
> I already ran some umbrella sampling simulations for the system, with
> differing simulations times per window and got very different results for
> free energy profile each time. (I did not carry out
> minimization,heat,equilbration in each window for these simulations. That
> may have been the issue.) I have attached them for reference (I have
> checked for convergence and that looks fine to me). Can anyone give me an
> idea about what's causing this issue? Thank you!
>
> Best
> Risi
>
>
>
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Received on Thu Jul 18 2024 - 12:00:02 PDT
