[gmx-users] I can't re-image molecule for multiple MD without trjcat them from start

[Asaminew Haile]

Hi Gromacs Users
I'm new for gromacs analysis

I'm running MD in a 40 ns time interval. I want to strip the water and
re-image the molecule. But I found that only if I trjcat all trajectories
from the start I can be able to re-image them.
Can someone show me how to re-image them independently?
Here is what I want

for every x in 1000
do
echo 1  | trjconv -s md.($x+40).tpr -f md.($x+40).xtc -o strip.($x+40).xtc
 -pbc nojump # strip water and re-image
done




thanks

ase