On 7/1/14, 11:28 PM, Chetan Mahajan wrote:
Thanks, Justin. *Until now, I was thinking that xtc coordinates are
wrapped. It's good to know that coordinates from xtc files are unwrapped
(please comment if not correct, since we talked only with respect to gro
That is correct. mdrun doesn't
Thanks a lot, Justin. It's much clearer, but one last question: If the
coordinates in sample.gro extracted from xtc trajectory using trjconv (
without any application of pbc) are unwrapped, why almost all of them
happen to lie in the box, as can be seen in the following snapshot? I would
expect
On 7/2/14, 6:45 PM, Chetan Mahajan wrote:
Thanks a lot, Justin. It's much clearer, but one last question: If the
coordinates in sample.gro extracted from xtc trajectory using trjconv (
without any application of pbc) are unwrapped, why almost all of them
happen to lie in the box, as can be
On 7/1/14, 9:08 PM, Chetan Mahajan wrote:
Thanks, Justin. Are you saying, the coordinates in .gro file extracted
from xtc trajectory are not wrapped, whereas those in the .gro file
generated at the end of gromacs MD run are wrapped in the box?
Yes, unless you've manipulated the trajectory
