Chandan - Hmm... What's the problem? template.c gives the numbers in NANOMETERS while PDB file contains them in ANGSTROMS.
To my knowledge, nowadays gromacs people use XDRFILE library to work with trajectories - http://www.gromacs.org/index.php?title=Download_%26_Installation -- Dr. Vitaly Chaban > Hello gmx users !! > > I was trying to use template.c. There I printed out the coordinates of a > trajectory file using the printf statement as under: > > printf("Coordinates at t=%8.3f : %8.5f %8.5f > %8.5f\n",fr.time,fr.x[n][XX],fr.x[n][YY],fr.x[n][ZZ]); > The output was > Reading frame 100 time 4400.000 Coordinates at t=4400.000 : 9.34053 > 4.26640 8.23887e > This is the output of the 4400.000 th time or 100th frame of the first Atom > in the trr file. > > Secondly, I dumped the 100th frame using tpbconv (of the same trajectory as > above) as: > trjconv -s *.tpr -f *.trr -dump 4400.00 -o frame100.pdb > > The frame100.pdb reads as: > > ATOM 1 N NGL A 1 93.405 42.664 82.389 1.00 0.00 > ATOM 2 H1 NGL A 1 93.849 42.216 81.599 1.00 0.00 > ATOM 3 H2 NGL A 1 93.914 43.464 82.737 1.00 0.00 > ATOM 4 H3 NGL A 1 93.577 41.958 83.090 1.00 0.00 > ATOM 5 CA NGL A 1 91.980 42.980 82.205 1.00 0.00 > ATOM 6 HA NGL A 1 91.538 41.996 82.050 1.00 0.00 > ATOM 7 CB NGL A 1 91.260 43.708 83.336 1.00 0.00 > ATOM 8 HB1 NGL A 1 90.206 43.782 83.068 1.00 0.00 > ATOM 9 HB2 NGL A 1 91.603 44.742 83.372 1.00 0.00 > > > We can clearly see the difference in the coordinates of the 1st Atom (ATOM 1 > N). > > That is the coordinates produced by the template are different than those of > trjconv's. > > Can someone help me out to correctly printf the x, y z coordinate using the > template.c file. > > Thanks > > Chandan -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
