[gmx-users] Bin files of g_sham

Thu Dec 19 08:39:18 CET 2013

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
> You're not asking it to read the bin index file in your command. Maybe
> 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
> >> about that? Could you please help me with that?
> >>
> >> 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
> >>>> --
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> >>>
> >>>
> >>> --
> >>> Ankita Naithani
> >>
> >>
> >>
> >> --
> >> Ankita Naithani
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> >
> > --
> > Ankita Naithani
> > --
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-- 
Ankita Naithani