[gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble

[Christian Bope Domilongo]

On 13 January 2016 at 22:22, luigi <luigi.capoferri at gmail.com> wrote:

> Hi,
>
> if your aim if to find out other conformational changes correlated to
> your CVs,
> you don't really need any reweighting of your trajectory: do a PCA on
> your trajectory and compare the projection of the frames with CV values
> of interest (according to your FES) on the new essential space.
>

I think I will just do PCA (g_covar), reweight the covariance matrix and
obtain modes


>
> If you well sampled your conformational space during the metadynamics
> you should probably discard the part in which the non-diffusive regime
> is reached: this would allow you to have a non-biased description of the
> possible conformational space along your CVs (no over-representation of
> the energy wells).


Technically, MDtraj can do that?


> You could also try to remove some noise and filter
> out frames with CV corresponding to high energietic conformations
> (keeping only relevant part of the FES).
> Then evaluate the projections of the frames with CVs of interest in the
> essential space obtained.
>
> How to do that technically.


> You should be able to obtain a fine description of what
> (conformationally) happen outside your explicitly defined collective
> variables.
>
> Cheers,
> Luigi
>
>
> On 13/01/16 14:09, Christian Bope Domilongo wrote:
> > Thank you Luiji,
> >
> >
> >
> > On 13 January 2016 at 20:51, luigi <luigi.capoferri at gmail.com> wrote:
> >
> >> Hi Christian,
> >>
> >> It is not so clear why do you want to have a "reweighted trajectory", in
> >> which you will likely lose all the maxima explored.
> >
> > In other word I want to get average trajectory canonical ensemble. The
> main
> > objective  to run g_covar, obtain the modes (eigenvalue and eigenvec) of
> my
> > metadynamics trajectory and compare it with NMA. The  challenge is I can
> > not compare directly because the trajectory  obtained  from plumed is
> not a
> > Boltzmann distribution that why I need to re-weight it first.
> >
> >
> >> However, if you want
> >> to extract the frames, e.g. related to a MEP, for, e.g. a nice movie,
> >> you could efficiently
> >> 1. evaluate the CVs values to extract analyzing the FES (and in case
> >> chose the number of frames for each value proportionally to the free
> >> energy of the system at those specific CVs),
> >> 2. select the frames based on the COLVAR files created by plumed and
> >> eventually
> >> 3 extract those frames from the TRR trajectory files.
> >>
> >> If you work in python I would suggest you to take a look at MDtraj
> >> library for extracting the frames.
> >>
> >> Cheers,
> >> Luigi
> >>
> >> On 13/01/16 12:23, Christian Bope Domilongo wrote:
> >>> Dear All,
> >>>
> >>> I have run my Metadynamics simulation perfectly using plumed. I have
> >> check
> >>> in the tutorial and website to find if it is possible to reweigh my
> meta
> >>> trajectory as a function of FES and obtain a average trajectory which
> is
> >> a
> >>> canonical ensemble. Because the trajectory  obtained  from plumed is
> not
> >> a
> >>> Boltzmann distribution.
> >>>
> >>> I have also us*e do *
> >>> HISTOGRAM
> >>>
> >>>
> http://plumed.github.io/doc-master/user-doc/html/_h_i_s_t_o_g_r_a_m.html
> >>> <
> >>
> http://www.google.com/url?q=http%3A%2F%2Fplumed.github.io%2Fdoc-master%2Fuser-doc%2Fhtml%2F_h_i_s_t_o_g_r_a_m.html&sa=D&sntz=1&usg=AFQjCNHvsK_WNA5VLHnvOijB6GKSrVOz7w
> >>>
> >>> with the REWEIGHT_BIAS option.
> >>>
> >>>
> >>> Regards,
> >> --
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> >
> >
>
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-- 
Bope Domilongo Christian
Ph.D candidate in Computational Biology
Division of Structural Biology and Biochemistry
School of Biological Sciences
Nanyang Technological University
Singapore
+6590565804
http://www.ntu.edu.sg/