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

[luigi]

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.

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). 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.

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,
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>

-- 
This e-mail, including any attachments, may contain private or confidential information.
If you think you may not be the intended recipient, or if you have received this e-mail in error, 
please contact the sender immediately and delete all copies of this e-mail.
If you are not the intended recipient, you must not reproduce any part of this e-mail or disclose 
its contents to any other party.