Dear All, Sorry for bothering you all, I was doing some mistake while doing cat, it is working fine.
sorry for the botheration, Pri... --- priyanka srivastava <[EMAIL PROTECTED]> wrote: > Dear All, > > I did a simulation of a lipid bilayer upto 10ns and > want to calculate its order parameter using g_order > analysis tools. Since it was restarted in the middle > so after the completion of 10ns I used cat command > to > combine the trr and tpr files to make one trr and > tpr > files for 10ns. > Also, by mistake I did not save the xtc file because > I > forgot to give the corresponding flag in the .mdp > file. > Now, when I issue the following command: > > g_order -f test.trr -n sn2.ndx -s test.tpr -b 0 -e > 1000 > > it reports: > > Reading frame 0 time 0.000 Number of > elements in first group: 48 > Reading frame 190 time 950.000 > > i.e. 10 frames or 50 ps less than what I specify. > If I change -e 1000 to 1005 then it looks fine: > > Reading frame 0 time 0.000 Number of > elements in first group: 48 > Last frame 200 time 1000.000 > > I am a little confused. Kindly tell me what is going > on here. I hope this is not because of of not saving > the xtc and hence not using it for g_order analysis. > Also, I tried using xtc file by using the trjconv > and > then running the same command but again the same > error > came up! > Also, when I run this command for complete 10ns trr > file (the one that I have made using cat), i.e. > using > -b 0 -e 10000, i get something like this: > > Reading frame 0 time 0.000 Number of > elements in first group: 48 > Last frame 2003 time 10000.000 > > Here 2003 frames is not clear to me. It should be > 2000 > only if I am not wrong. > > Kindly suggest me something. > waiting eagerly for the reply, > Pri... > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam > protection around > http://mail.yahoo.com > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
