# [gmx-users] Bin files of g_sham

bipin singh bipinelmat at gmail.com
Thu Dec 19 13:26:51 CET 2013

```Since you already built 2-d free energy landscape (FEL), you should
have PCs (PC1 and PC2) as a function of time. You also know from the
minima of FEL at which PCs the system spends longer time. Once you
find those PCs you should find when the system has those PCs (from PC
vs time). Then you should visualize your trajectory and check the
structures at those periods of time. Once you collect all the
structures you can pick the representative structure.

On Thu, Dec 19, 2013 at 1:09 PM, Ankita Naithani
<ankitanaithani at gmail.com>wrote:

> Hi Llyod,
>
> Thank you very much indeed for your kind involvement in answering my
> question. Yes, I did tell g_sham not expect the time while I issued the
> command to run it. Yes, I have done PCA already on my trajectory, could you
> just guide  me a little further as to what is the technique which can help
> me to look at the frames corresponding to the the energy? Meanwhile, I
> shall also try to grasp your advice/suggestions and see how far can I make
> my little brain work towards it.
>
> Kind regards,
>
> Ankita
>
>
> On Thu, Dec 19, 2013 at 2:49 AM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:
>
> > Trying to help I would say I am trying to remember some things I did some
> > time ago.  That said, your missing the time column as your first input.
> > You are making a 2D energy plot is what your telling it to do, you can
> also
> > tell it not to expect a time which would be correct for your case,
> however
> > this is a landscape your generating.  It is already a total energy
> > landscape in 1 nm by 2 nm 2D volumn, what your doing is trying to use the
> > boltzman inversion equation in the g_sham to break it down into gibbs,
> enth
> > and entro as .xpm plots.  Your bins are the "pixels" or points in the
> > landscape I believe, thus the binwidth is the xmin and max, but I amnot
> > 100% sure how the numbering goes. You can check it against the image file
> > generated (look at it with gedit, the pixel portion will tell you).
> >
> > One way to get it to work, would be to supply a free energy single column
> > (or time, then single energy column), however someone might  correct me
> on
> > this (I hope) if I am wrong.
> >
> > However your origional question was to look up or coordinate a line graph
> > gibbs energy plot, with a frame in your trajectory.  Thus I believe you
> > want to look at a linear plot of your energy change over time.  If you
> > generated the eigen vectors already, there are methods in these
> techniques
> > to look at frames versus energy (total).  You can also if you designed
> your
> > experiment as a pulled/steered free energy experiment, use the g_wham,
> with
> > no bootstraping or autocorrelation, etc...with one trajectory, and it is
> a
> > sham.  Otherwise, your using the wrong things to get what you want (g_
> > scripts in gromacs), and need to read the manual again.  You can, with an
> > index for only what you want, extract total energy and plot it as well
> > versus frame, which might give you what you want also...using just
> g_energy.
> >
> > I hope that helps,
> >
> > Stephan Watkins
> >  *Gesendet:* Donnerstag, 19. Dezember 2013 um 00:09 Uhr
> > *Von:* jkrieger at mrc-lmb.cam.ac.uk
> > *An:* "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> > *Betreff:* Re: [gmx-users] Bin files of g_sham
> > that explains what you're seeing?
> >
> > On 18 Dec 2013, at 13:51, Ankita Naithani <ankitanaithani at gmail.com>
> > wrote:
> >
> > > Hi Lloyd,
> > >
> > > So, my input to g_sham is a file with following lines:
> > >
> > > @ title "2D projection of trajectory"
> > > @ xaxis label "projection on eigenvector 1 (nm)"
> > > @ yaxis label "projection on eigenvector 2 (nm)"
> > > @TYPE xy
> > > 0.16750 0.18278
> > > -0.01448 -0.14834
> > > -0.32757 0.22259
> > > -0.33832 0.63817
> > >
> > > This file is named AM_12.xvg
> > >
> > > and my command line is g_sham -f AM_12.xvg -ls AM_FEL_12.xpm
> > >
> > > My bin index file has the following lines:
> > >
> > > [ 18 ]
> > > 7105
> > > [ 19 ]
> > > 7104
> > > [ 46 ]
> > > 7124
> > > [ 48 ]
> > > 7123
> > > [ 49 ]
> > > 7106
> > > [ 50 ]
> > > 6497
> > > 6498
> > > [ 51 ]
> > > 6499
> > > 6500
> > > [ 52 ]
> > > 6496
> > > 7103
> > > [ 53 ]
> > > 7102
> > > [ 55 ]
> > > 6672
> > > [ 75 ]
> > > 5745
> > > 5749
> > > and so on.
> > >
> > > I am not sure how can I look at the default binwidth.
> > >
> > > Kind regards,
> > >
> > > Ankita
> > >
> > >
> > > On Tue, Dec 17, 2013 at 6:03 PM, lloyd riggs <lloyd.riggs at gmx.ch>
> wrote:
> > >
> > >>
> > >> You need to explain what you are doing better, what you want to do,
> and
> > >> show your input (command line, .xvg lines of input and output as
> > example)
> > >> and you might get more help on here. If you read the -h from g_sham,
> it
> > is
> > >> making a single plot from your input, and in this case your .xpm would
> > be a
> > >> matrix with bins on a 2D surface with points taken across the entire
> > run,
> > >> as an example of what I mean. I believe you can also use a single line
> > >> (time, energy as column 2), and get a single line out as well, with a
> > >> meaningless "landscape" still put out as .xpm, etc...look at your
> > binwidth
> > >> default, input and what you want out is all I could say at this point.
> > You
> > >> might be trying to do something else however...
> > >>
> > >> Stephan
> > >> *Gesendet:* Dienstag, 17. Dezember 2013 um 08:38 Uhr
> > >>
> > >> *Von:* "Ankita Naithani" <ankitanaithani at gmail.com>
> > >> *An:* "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > >> *Betreff:* Re: [gmx-users] Bin files of g_sham
> > >> I would like to add that maybe the bins store Frame numbers. Because I
> > seem
> > >> to have around 21000 frames and I guess I am unable to see a number
> > higher
> > >> than that. Apologies for the confusion about earlier number. So, in
> this
> > >> case if I want a confirmation at a particular frame number, how should
> > I go
> > >>
> > >> Kind regards,
> > >>
> > >> Ankita
> > >>
> > >>
> > >> On Tue, Dec 17, 2013 at 7:20 AM, Ankita Naithani
> > >> <ankitanaithani at gmail.com>wrote:
> > >>
> > >>> Hi Llyod,
> > >>>
> > >>> Thank you for your reply. I actually wanted to extract frames
> > >>> corresponding to the g_sham output. The input for g_sham in my case
> was
> > >>> column 1 had time points, column 2 and column 3 had Principal
> > component 1
> > >>> and Principal component 2 respectively. So, the binning which has
> been
> > >>> done, i.e. if I say that the bin number 786 has the following few
> > numbers
> > >>> like : 3876, 9870, 22002 etc. These should technically correspond to
> > the
> > >>> time points right which I can then dump using trjconv too maybe.
> > >>>
> > >>> Also, I am a little confused because if the bins have all the time
> > >> points,
> > >>> I don't seem to find the time points uptil the end of simulation in
> > that
> > >>> case i.e. I am unable to see higher time scale. My simulation was for
> > >> 48ns
> > >>> and had 3fs time step. I am unable to trace anything beyond 22000 or
> > >> 23000
> > >>> number in my bins.
> > >>>
> > >>> I hope you could help me solve this confusion.
> > >>>
> > >>> Kind regards,
> > >>>
> > >>> Ankita
> > >>>
> > >>>
> > >>> On Sun, Dec 15, 2013 at 11:17 PM, lloyd riggs <lloyd.riggs at gmx.ch>
> > >> wrote:
> > >>>
> > >>>>
> > >>>> I will attempt an answer, however there might be a better response.
> It
> > >>>> depends on your input .xvg (what the first column is) and what you
> are
> > >>>> telling it to do (defualt is time), and if these correspond to your
> > time
> > >>>> frames (can be timepoint or siply frame # I believe). g_sham seems
> (to
> > >> me)
> > >>>> to work like a comand line spread sheet manipulator with some built
> in
> > >>>> functions. If you want a particular frame from a trajectory time
> > point,
> > >>>> then use g_traj with the first/last set to the frame you want but
> > >> there's
> > >>>> also 2 other tools that do this the same way...
> > >>>>
> > >>>> Stephan Watkins
> > >>>> *Gesendet:* Sonntag, 15. Dezember 2013 um 14:49 Uhr
> > >>>> *Von:* "Ankita Naithani" <ankitanaithani at gmail.com>
> > >>>> *An:* "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > >>>> *Betreff:* [gmx-users] Bin files of g_sham
> > >>
> > >>>> Hi,
> > >>>>
> > >>>> I had a query regarding the bin files generated by g_sham.
> > >>>> Does the bin index contain timepoints? i.e. there are 1024 bins so
> > each
> > >>>> bin
> > >>>> has a number of time points? And supposes bin 756 has numbers like
> > 3876,
> > >>>> 20020, 7896 so these would all correspond to time and we could then
> > dump
> > >>>> the representative frame corresponding to these time points?
> > >>>>
> > >>>> I am a little confused as to what is stored in the bins? Timepoints
> or
> > >>>> frame number and then alternatively how to get the representative
> > >>>> frame/snapshot stored at that specific bin number.
> > >>>>
> > >>>> Kind regards,
> > >>>>
> > >>>> --
> > >>>> Ankita Naithani
> > >>>> --
> > >>>> Gromacs Users mailing list
> > >>>>
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> > >>>
> > >>>
> > >>> --
> > >>> Ankita Naithani
> > >>
> > >>
> > >>
> > >> --
> > >> Ankita Naithani
> > >> --
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> > >
> > >
> > > --
> > > Ankita Naithani
> > > --
> > > Gromacs Users mailing list
> > >
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>
> --
> Ankita Naithani
> --
> Gromacs Users mailing list
>
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--

*--------------------Thanks and Regards,Bipin Singh*
```