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

[Christian Bope Domilongo]

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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-- 
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/