I have recently started using LAMMPS. I am doing NPT simulation on polymers in a water box. I have a fairly large system with close to 50000 atoms. There is no coarse-graining involved, I used all-atom force fields.
I did 4 consecutive runs of 5ns each as a result I have 4 trajectories files for 5ns,10ns,15ns and 20ns. Since I used data files generated at the end of each simulation as the input for the next run, all my trajectory files start at timestep 0.
I used rerun to calculate rdf in the following manner:
boundary p p p
pair_style lj/cut/coul/long 15.0
pair_modify tail yes
special_bonds lj/coul 0 0 0.5
kspace_style pppm 0.00001
variable nevery index 500
variable nrepeat index 500
variable nfreq index 500000
variable nbins index 500
variable trjtimesteplast index 2500000
variable molname index 10napss36f1wat_spc_160mMnacl