[gmx-users] Bin files of g_sham

[Ankita Naithani]

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