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