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<div>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...</div>
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<div>Stephan</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Dienstag, 17. Dezember 2013 um 08:38 Uhr<br/>
<b>Von:</b> "Ankita Naithani" <ankitanaithani@gmail.com><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
<b>Betreff:</b> Re: [gmx-users] Bin files of g_sham</div>
<div name="quoted-content">I would like to add that maybe the bins store Frame numbers. Because I seem<br/>
to have around 21000 frames and I guess I am unable to see a number higher<br/>
than that. Apologies for the confusion about earlier number. So, in this<br/>
case if I want a confirmation at a particular frame number, how should I go<br/>
about that? Could you please help me with that?<br/>
<br/>
Kind regards,<br/>
<br/>
Ankita<br/>
<br/>
<br/>
On Tue, Dec 17, 2013 at 7:20 AM, Ankita Naithani<br/>
<ankitanaithani@gmail.com>wrote:<br/>
<br/>
> Hi Llyod,<br/>
><br/>
> Thank you for your reply. I actually wanted to extract frames<br/>
> corresponding to the g_sham output. The input for g_sham in my case was<br/>
> column 1 had time points, column 2 and column 3 had Principal component 1<br/>
> and Principal component 2 respectively. So, the binning which has been<br/>
> done, i.e. if I say that the bin number 786 has the following few numbers<br/>
> like : 3876, 9870, 22002 etc. These should technically correspond to the<br/>
> time points right which I can then dump using trjconv too maybe.<br/>
><br/>
> Also, I am a little confused because if the bins have all the time points,<br/>
> I don't seem to find the time points uptil the end of simulation in that<br/>
> case i.e. I am unable to see higher time scale. My simulation was for 48ns<br/>
> and had 3fs time step. I am unable to trace anything beyond 22000 or 23000<br/>
> number in my bins.<br/>
><br/>
> I hope you could help me solve this confusion.<br/>
><br/>
> Kind regards,<br/>
><br/>
> Ankita<br/>
><br/>
><br/>
> On Sun, Dec 15, 2013 at 11:17 PM, lloyd riggs <lloyd.riggs@gmx.ch> wrote:<br/>
><br/>
>><br/>
>> I will attempt an answer, however there might be a better response. It<br/>
>> depends on your input .xvg (what the first column is) and what you are<br/>
>> telling it to do (defualt is time), and if these correspond to your time<br/>
>> frames (can be timepoint or siply frame # I believe). g_sham seems (to me)<br/>
>> to work like a comand line spread sheet manipulator with some built in<br/>
>> functions. If you want a particular frame from a trajectory time point,<br/>
>> then use g_traj with the first/last set to the frame you want but there's<br/>
>> also 2 other tools that do this the same way...<br/>
>><br/>
>> Stephan Watkins<br/>
>> *Gesendet:* Sonntag, 15. Dezember 2013 um 14:49 Uhr<br/>
>> *Von:* "Ankita Naithani" <ankitanaithani@gmail.com><br/>
>> *An:* "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
>> *Betreff:* [gmx-users] Bin files of g_sham<br/>
>> Hi,<br/>
>><br/>
>> I had a query regarding the bin files generated by g_sham.<br/>
>> Does the bin index contain timepoints? i.e. there are 1024 bins so each<br/>
>> bin<br/>
>> has a number of time points? And supposes bin 756 has numbers like 3876,<br/>
>> 20020, 7896 so these would all correspond to time and we could then dump<br/>
>> the representative frame corresponding to these time points?<br/>
>><br/>
>> I am a little confused as to what is stored in the bins? Timepoints or<br/>
>> frame number and then alternatively how to get the representative<br/>
>> frame/snapshot stored at that specific bin number.<br/>
>><br/>
>> Kind regards,<br/>
>><br/>
>> --<br/>
>> Ankita Naithani<br/>
>> --<br/>
>> Gromacs Users mailing list<br/>
>><br/>
>> * Please search the archive at<br/>
>> <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List</a> before<br/>
>> posting!<br/>
>><br/>
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>> --<br/>
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>> posting!<br/>
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>><br/>
>><br/>
><br/>
><br/>
> --<br/>
> Ankita Naithani<br/>
><br/>
<br/>
<br/>
<br/>
--<br/>
Ankita Naithani<br/>
--<br/>
Gromacs Users mailing list<br/>
<br/>
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List</a> before posting!<br/>
<br/>
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