Many thanks to both of you! :)
I am not that familiar with C-Code and gromacs. Maybe you could take a look
at it, that this would be correct for me? Does this code also work for none
cubic boxes?
// Here begins the actual analysis
static int analyze_frame(t_topology *top, t_trxframe *fr, t_pbc
Hi :)
I am having a little problem with my cubic box full of water. I am trying to
calculate the polarization density so I divide the box into different layers
in Z-direction and do my calculation for every layer. The box goes from 0 nm
to 4 nm in every direction. Now I realized that some of my
Justin Lemkul wrote
Well, what did you do to observe negative coordinates? In principle, all
unit
cells in Gromacs have an origin at (0,0,0) and the way mdrun works you
should
only get positive coordinates, IIRC. So the emergence of negative
coordinates
is a bit odd, but there's
OK, just in case I just want the atoms in the box and I don't care about
Molecules, this should work?
trjconv -f traj.trr -o traconv.trr -pbc atom
Because I tried and it does SOMETHING. Some atoms are in the box now (I
guess) but still atoms are out of the box. Do I have to add some commands?
