you perform wham the same as with the normal umbrella sampling, using data
from all of the windows at the same time.
if you are using Alan Grossfield's code, for example, the lines in the
meta.in file correspond to the different Hs.
for analysis there is no difference between umbrella sampling and
HREMD umbrella sampling. WHAM does not need to be told that the windows
were generated with HREMD to improve sampling.
On Fri, Sep 6, 2024 at 9:46 AM miyagi bunkutu <miyagi_b.yahoo.com> wrote:
> But if I were to perform. WHAM on each trjectory seperately I will end up
> with multiple pmf lanscapes. (Each for multiple trajectories) How can I
> make this a combined single landscape? (As in the case of normal umbrella
> sampling?)
>
> On Friday, September 6, 2024 at 08:35:26 AM CDT, Carlos Simmerling via
> AMBER <amber.ambermd.org> wrote:
>
>
> 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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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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Received on Fri Sep 06 2024 - 07:00:02 PDT
