Tutorial
Extended Lagrangian MD simulation of GAGTACTC DNA duplex in the box of water
using Drude polarizable CHARMM force field

Input files:
dna_drudemd_1c3_cf1c_eq.inp - system equilibration with harmonic constraints on DNA atoms except for Drudes
dna_drudemd_1c3_cf1c_pr.inp - production run without constraints

Initial coordinate files
md_gagtactc_bform_300mm.crd       - hydrated DNA molecule from CHARMM27 simulation (not used)
md_gagtactc_bform_300mm_dna.crd   - DNA molecule only 
md_gagtactc_bform_300mm_sod.crd   - Na+ ions
md_gagtactc_bform_300mm_water.crd - SWM4 water molecules

toppar/ folder includes topology and parameter files as well as stream files
used for charge and polarizability assignment
toppar/top_all27_na_drude_1c3.rtf - main topology file
toppar/par_all27_na_drude_1c3.prm - main parameter file
toppar/toppar_drudes_na.str       - auxillary topology/parameter file for Drude particles
toppar/toppar_swm4_ions.str       - auxillary topology/parameter file for SWM4 water and Na+ ions
toppar/dna_setpol_cf1c.str        - charges/polarizabilities for DNA (main file)
toppar/ade_dna_setpol_cf1c.str    - charges/polarizabilities for adenine base
toppar/cyt_dna_setpol_cf1c.str    - charges/polarizabilities for cytosine base
toppar/gua_dna_setpol_cf1c.str    - charges/polarizabilities for guanine base
toppar/thy_dna_setpol_cf1c.str    - charges/polarizabilities for thymine base
toppar/phos_dna_setpol_cf1c.str   - charges/polarizabilities for phosphodiester
toppar/deri_dna_setpol_cf1c.str   - charges/polarizabilities for deoxyribose backbone
toppar/termoh_dna_setpol_cf1c.str - charges/polarizabilities for terminal OH groups
toppar/polar_swm4_ions.str        - charges/polarizabilities for SWM4 water and Na+ ions

out/ folder, which contains all output files

*.trj - trajectory files
*.rst - restart file
*.ene - energy files
*.crd - CHARMM coordinate files
*.pdb - protein data bank files 

gagtactc_1c3_cf1c_eq_harm* - equilbration run
gagtactc_1c3_cf1c_pr_*     - production run