the trajectory files from HREMD are written separately for each Hamiltonian
(in your case, for each umbrella window). These can be processed the same
way as if they were done via standard umbrella sampling, so your previous
analysis methods should work here too. There is no need to sort the log
file. If you are using WHAM, then use the restraint values saved from each
replica just as you use the ones saved from the normal restrained MD.
On Fri, Sep 6, 2024 at 9:32 AM miyagi bunkutu <miyagi_b.yahoo.com> wrote:
>
> Thanks for the reply. I have run the simulation. Its the analysis part
> that I am not familiar with. My current idea is to separate the
> trajectories in to each bias umbrella window, (i.e. ith generated
> trajectory file corresponds to frames with ith umbrella window's biasing
> potential) and then do the analysis (that is how I do regular remd
> analysis). But I am not sure how to incorporate WHAM into this method. Am I
> to somehow sort the restraint log likewise (window wise) and then perform
> wham for each window? But that does not make much sense. I tried looking
> for literature but could not find anything useful with detailed analysis
> procedure. Maybe I am not using the correct keywords. Any help on the
> matter is really appreciated.
> On Sunday, September 1, 2024 at 07:01:08 AM CDT, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>
> 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 Fri Sep 06 2024 - 07:00:02 PDT
