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

[luigi]

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. 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,