[gmx-users] Re: xdrfile library, read co-ordinates from .xtc

Vitaly V. Chaban vvchaban at gmail.com
Tue Aug 11 22:11:09 CEST 2009

Hi Lipi,

What do you mean saying that the coordinates are random?

You can access the coordinates of the particular atom with
x_xtc[i][j], where "i" is a number of atom in a system, "j[0]" - is
x-coord, j[1] - y-coord, j[2] - z-coord. The same logic relates to
reading trr files.


> I have downloaded xdr library to read .xtc files.
> The installation of the xdrlibrary worked without any problems. The
> compilation of the test program "trr2xtc.c" also worked.
> Now I'm trying to store the coordinates of a xtc trajectory into a local
> variable. I first tried to print out the coordinates. I just modified the
> trr2xtc code. Here a few line of my code:
>  xd_read = xdrfile_open(rfile, "r");
>  x_xtc = calloc(natoms_xtc, sizeof (x_xtc[0]));
>  result_xtc = read_xtc(xd_read, natoms_xtc, &step_xtc, &time_xtc, box_xtc, x_xtc, &prec_xtc);
>  printf("%f %f %f\n",x_xtc[0],x_xtc[1],x_xtc[2]);
> The coordinates in the variable x_xtc seems to be random. How do I access
> the proper coordinates from the trajectory?
> I would appreciate any help.
> Thanks,
> Lipi

Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua,vvchaban at gmail.com
skype: vvchaban, cell.: +38-097-8259698
!!! Looking for a postdoctoral position !!!

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