[gmx-users] Bin files of g_sham

Thu Dec 19 00:12:27 CET 2013

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
>>>> --
>>>> Gromacs Users mailing list
>>>> 
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>>> 
>>> 
>>> --
>>> Ankita Naithani
>> 
>> 
>> 
>> --
>> Ankita Naithani
>> --
>> Gromacs Users mailing list
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> 
> 
> -- 
> Ankita Naithani
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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