[gmx-users] Bin files of g_sham

Ankita Naithani ankitanaithani at gmail.com
Wed Dec 18 14:51:59 CET 2013 

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
> >> --
> >> Gromacs Users mailing list
> >>
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> >
> >
> > --
> > Ankita Naithani
> >
>
>
>
> --
> Ankita Naithani
> --
> Gromacs Users mailing list
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-- 
Ankita Naithani

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