// Try some molecular dynamics with NAB and HCP=4

molecule m;
float x[dynamic], f[dynamic], v[dynamic];
float fret;

// Create a molecule from a pdb file and a force-field parameter file.

m = getpdb( argv[2] + "_min.pdb");
allocate x[ 3*m.natoms ];
allocate f[ 3*m.natoms ];
allocate v[ 3*m.natoms ];
readparm( m, argv[2] + ".prmtop" );
getxv(  argv[2] + "_min.rst7", m.natoms, fret, x, v );

// Initialize molecular mechanics..
mm_set_checkpoint(argv[2]+".%d.x");
mm_options("ntwx=5000, dt = 0.002, gb=8, gbsa=1, hcp=4, dhcp=0.25, nscm=500, nchk=1000");
mme_init(m, NULL, "::ZZZZ", x, "traj");

// Do some molecular dynamics.

mm_options("gamma_ln=1.0, temp0=298.0, tempi=298.0, ntpr=5000, epsext=78.5");
md(3*m.natoms, 500000, x, f, v, mme);
mme_timer();