[gmx-users] Bin files of g_sham

Ankita Naithani ankitanaithani at gmail.com
Tue Dec 17 08:21:17 CET 2013


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


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