I have a doubt about the position dump file i am getting after using minimize command.The positions that are dumped at each snap are the energy minimized(at each step) position of landscape of the real trajectory or the energy of the system is minimized at once,then its trajectory is dumped in the dump file?
I hesitate to reply but I suspect that "minimize" does not create dump
files. I know that "run" does. If you want to save the coordinates
after minimization in dump format, then I think you could add a "run"
command after the "minimize" command. The end of the in.rerun input
script would look something like this:
minimize 1.0e-5 1.0e-7 500 2000
fix 1 all nve
dump 1 all custom 1 dumpfile.lammpstrj id mol type x y z ix iy iz
(If that does not work, replace "run 0" with:
(Be sure to eliminate any other "run" commands from your input script
may have located before the minimize command.)
I'm curious to see how you did this, once you have ironed out all the details.
You can do dumps during a minimization. The iterations
of the minimizers are treated like timesteps, so if you
do a dump every timestep, you will get the positions
of the atoms at every iteration. You will also get
a dump snapshot at the end of the minimization. The
dump doc page explains this.