yes, you can use the HREMD facility to run umbrella sampling simulations.
Each replica (H) wil have a different mdin file (or different set of
restraints read by that mdin file). and yes you can use WHAM to process the
results. There are other ways to process umbrella sampling, but there are
papers in the literature about this and it isn't Amber-specific.
On Thu, Aug 29, 2024 at 3:07 PM miyagi bunkutu via AMBER <amber.ambermd.org>
wrote:
> Hello,
> I am trying to run Replica Exchange Umbrella Sampling along a reaction
> coordinate for a molecule. I have run both Umbrella sampling and REMD
> simulations separately before, but never together. My idea is to create
> replicas at different points on the reaction coordinate (i.e. chosen angle
> at 180,175,170..... etc) and run H-REMD (remd=3) with added harmonic
> restraints (like in umbrella sampling).
> Is this the correct workflow?If not can anyone suggest me a tutorial or a
> paper that describes a clear workflow?
> Also I normally use a WHAM to create the PMF of the umbrella sampling. But
> I don't think I can use it directly here. I would really appreciate it, if
> someone can give me an idea or suggest a tutorial about the post-processing
> and analysis of this kind of a simulation. Any response is highly
> appreciated. Thanks!
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Received on Sun Sep 01 2024 - 05:30:02 PDT
