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 -- 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.