1.  Setup the solvent box, the DNA structure and merge systems
     to create solvated DNA with counterions
 

Input files:

waterbox_prep.inp   (Generates solvent box; can also be used to generate a sphere of solvent)
top_all27_na.rtf       (the CHARMM topology file)
par_all27_na.prm     (the CHARMM parameter file)
TIP32.CRD              (coordinates of a 216 TIP3P water molecules)
wat_sod_1b.crd        (water box with sodium ions)
 
 

gen_overlay.inp                 (generates DNA system coordinate and psf file)
top_all27_na.rtf                 (the CHARMM topology file)
par_all27_na.prm              (the CHARMM parameter file)
deo_1a.crd                         (DNA coordinates)
wat_sod_30_18_18.crd     (coordinates of water box with sodium ions)

gen_overlay_test.inp        (test of image generation by crystal)

2. Initial minimization and dynamics to equilibrate solvent around DNA
 

dyn_harm_1a.inp       (20 ps NVT simulation with DNA constrained to allow solvent
                                     to equilibrate around the DNA)

3. Production dynamics

dyn_pme_1a.inp      (MD on 5'-cgcgaattcgcg-3' ecor1 dna duplex in a box of water
                                  and counterions Particle Mesh Ewald to treat long range electrostatics,
                                  NPT ensemble via the Langevin Piston)

4. Trajectory Analysis

 
ana_dyn_puck.inp
ana_dyn_sug_ang.inp
ana_dyn_sug_dihe.inp
bkb_dihedral_corr.inp
dist_bp_1.inp
hydr_dna_1.inp
rms_vs_ideal.inp
solv_dna_inter_1.inp