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 <ankitanaith...@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.ri...@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" <ankitanaith...@gmail.com> >> *An:* "Discussion list for GROMACS users" <gmx-us...@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 >> <ankitanaith...@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.ri...@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" <ankitanaith...@gmail.com> >>>> *An:* "Discussion list for GROMACS users" <gmx-us...@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 >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>>> >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> >>> -- >>> Ankita Naithani >> >> >> >> -- >> Ankita Naithani >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. > > > -- > Ankita Naithani > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.