This page is about setup and running of water solution using charmm, including pure water box and ionized water box.
the path for the simulation is:
The input file water.inp is from http://pages.jh.edu/~rschlei1/Random_stuff/charmmscripts/waterbox.inp.
charmm < water.inp
This will creat a water box which has 21*21*21=9261 water molecules. output files:water_box.pdb/crd.
We minimize the system and then slowly heating the water box from 50K to 300K for 20000 steps. echeck=100000.
mpirun -np 12 charmm < heat_equi_nvt.inp
Then run production simulation for 1000 steps. nsavc=1. dyna restart from previous equilibration. echeck=1000.
mpirun -np 12 charmm < md.inp