[gmx-users] coordinates file format
mark.j.abraham at gmail.com
Tue Jan 27 10:32:26 CET 2015
On Tue, Jan 27, 2015 at 10:01 AM, mah maz <mahmaz71 at 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
> 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!
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.
> I appreciate your help as usual. thanks alot!
> On Mon, Jan 26, 2015 at 8:01 PM, mah maz <mahmaz71 at 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,
> > 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 <mahmaz71 at 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
> >> 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
> >> 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 <mahmaz71 at 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
> * 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-request at gromacs.org.
More information about the gromacs.org_gmx-users