On Tue, Jan 27, 2015 at 10:01 AM, mah maz <mahma...@gmail.com> wrote:
> Dear Justin and Mark, > > I think you are both right. > > I didn't get your last sentence Mark! What is a libxdrfile? > Ask google ;-) It's a library distributed from the GROMACS website to make it easier to read files into C and (particularly) Fortran programs. > Justin, The problem is I have so many atoms in the system. As I said the > best format for reading data is to be like this: > time x1 y1 z1 x2 y2 z2 ....... xn yn zn > 0 1 2 3 2 3 4 8 5 6 > 0.1 > 0.2 > ... > as you know the trajectory format is like this: > > (t=)0 x1 y1 z1 x2 y2 z2 x3 y3 z3 x4 y4 z4....... > x5 y5 z5 ......... x4000 y4000 z4000 > (t=)0.1 x1 y1 z1 x2 y2 z2.............. > x5 y5 z5 ....... x4000 y4000 z40000 > completely difficult and confusing for me and the program both! > The following pseudocode reads both, because they're the same thing! ignore_useless_title_row_if_present() for frame (1 .. end of file) frametime[frame] = read_next_number() for atom (1 .. number_of_atoms) for dim (x y z) framecoords[atom][dim] = read_next_number() The field widths are fixed, so this probably even works in Fortran. According to your points, I can come to the conclusion that changing the > file format is not possible. > It's perfectly possible to write a script to transform it to whatever you like. But that would serve no useful purpose. Mark > I appreciate your help as usual. thanks alot! > > Cheers, > Mah > > > > > > > > On Mon, Jan 26, 2015 at 8:01 PM, mah maz <mahma...@gmail.com> wrote: > > > Dear Mark, > > > > Thanks for your reply. I think it is not! I have 4000 atoms, the first > > number is time, then 4000 x y and z: x1,y1,z1, x2, y2, z2, ....,x4000, > > y4000, z4000. They are following each other not in a special order. Then > > the next time step starts with x1,y1,z1,....,x4000, y4000, z4000. So, > they > > are not in a column as they are supposed to be. Can I do anything to a > > result file to be in my preferable format? > > > > Many Thanks! > > Regards, > > Mah > > > > On Mon, Jan 26, 2015 at 12:08 PM, mah maz <mahma...@gmail.com> wrote: > > > >> Hi Mark, > >> I want to have X Y Z of each atom for all time step apart from other > >> atoms so that I can use them as data for programing; like this for > instance: > >> t x1 y1 z1 x2 y2 z2 > >> 0 2.4 3.5 4.5 5.6 7.9 9.8 > >> 0.1 5.5 6.7 8.9 > >> ... > >> in which 0 and 0.1 are time and the rest are x1 y1 z1 of the 1st atom > and > >> x2 y2 z2 are for the 2nd atom. > >> Is it possible to get the file in a desired format? > >> thank you! > >> > >> On Mon, Jan 26, 2015 at 11:54 AM, mah maz <mahma...@gmail.com> wrote: > >> > >>> Dear all, > >>> > >>> I have extracted a file of coordinates after a simulation with 1000000 > >>> steps writen every 1000 steps, by "g_traj -s -ox" . The result is a > file in > >>> which the first column is time and all coordinates are following it. Is > >>> there a way that I can get coordinates of each time step in a more > >>> classified way? > >>> > >>> Thanks! > >>> > >> > >> > > > -- > 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.