Hi,
I have a piece of code in C that is supposed to write atom coordinates
in xtc format. I want to use the xtcio functions from the gromacs
library. I use open_xtc() and close_xtc() at the beginning and end of my
code. Between them I have multiple calls to write_xtc(), one for each
frame. I wrote a wrapper function to convert my own datatypes (see below).
Now I experience very weird behaviour: When I have up to 9 atoms of
which I want to write the coordinates everything is fine (VMD can
visualize the trajectory properly). From the 10th atom on the actual
length of the xtc file is shorter than the one with less atoms and VMD
has trouble interpreting its contents, i.e. it sets all coordinates to
zero for all frames. So obviously something is really wrong here.
Does anyone have an idea what I am doing wrong?
Cheers,
Oliver
void write_frame(t_fileio * XTCfile, // pointer to open xtc file
float * r, // coordinate vector of length
int natoms, // number of atoms
float * L, // cubical box length
int step, // frame number
float time) { // simulation time
int dim = 3; // space dimensions
matrix box = {{L[0], 0.0, 0.0},
{0.0, L[1], 0.0},
{0.0, 0.0, L[2]}}; // box vectors
real prec = 0.00001; // I don't get the purpose of this one
// convert data from simple array to rvec[DIM] vectors used by gromacs
rvec xrvec[natoms];
int i, j;
for (i=0; i < natoms; i++) {
for (j=0; j < dim; j++)
xrvec[i][j] = r[i*dim + j];
}
write_xtc(XTCfile, natoms, step, time, box, xrvec, prec);
}
--
Oliver Schillinger
Master's student
Forschungszentrum Juelich GmbH
52425 Juelich | Germany
Building 5.8v, Room 3010
Phone: 02461-61-9532
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
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