I will try to offer some advice, though many others probably will have
helpful comments too.
you should not need to redo the minimization and heating if you are simply
taking the restart and moving to the next window. Since you change the
restraint target, I think it does make sense to do some short MD with the
new restraints before you start collecting data for the new window. how
long that needs to be will probably depend on how large a change you made
from the prior window.
for your free energy profiles, they also look quite noisy and you don't say
anything about how you calculated them.
for a recent example of umbrella sampling for a base unstacking in both
explicit and implicit water, look at this article (details are in the SI)
https://pubs.acs.org/doi/full/10.1021/acs.jcim.4c00756
you will want to check the overlap of sampling between neighboring windows,
and perhaps also look at the time dependence of things in each window so
you can be confident that the profile is adequately sampled. also look at
the rest of your system - you want to be confident that the RC is a good
one, and that other motions in the system are not slow on the timescale of
each window.
On Thu, Jul 18, 2024 at 2:44 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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>
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Received on Thu Jul 18 2024 - 12:00:03 PDT
