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.