Dear lammps users
I want to get whole molecules in VMD. I dump out my trajectories by following commands
dump 1 all custom 100 coro-x.lammpstrj id type q x y z ix iy iz mass element vx vy vz
dump_modify 1 element C H O
Thus vmd can get more information (including the elements name) about my systems.
Then and then I loaded the coro-x.lammpstrj to vmd. To wrap molecules to box, I typed following commands in TK console
pbc wrap -compound res -all
At first 3000 frames, the molecules are in box and the molecules are intact. However, the molecules are out box after 3000 frames.
Then I deleted the all frames. And then I reloaded the trajectory to vmd, followed by typing following commands.
pbc wrap -compound fragment -all
The same problems occured again (The molecules are in the box at first 3000 frames and out of box after that).
My guess is that my dump file is too big (I have loaded 15000 frames) to be handled by VMD, so the “wrap –compound” command just works for the first 3000 frames. (I am not sure about my guess.)
I want to split the dump file to several small parts and retry it with “wrap –compound” command
to see whether I can get the get whole molecules or not in all frames. My first try was to load the frames to pizza.py and split it. I have tried dump tool in pizza.py with following commands
read 0 snapshots
0 snapshots selected out of 0
assigned columns: id type q x y z ix iy iz mass element vx vy vz
It seems there are no frames.
My question is
how can I split dump file generated by lammps?