// Try some newton-raphson minimization

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

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

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

// Initialize molecular mechanics..

mm_options("cut=9999.0, rgbmax=9999.0, ntpr=1, nsnb=9999, gb=1, diel=C" );
mme_init(m, NULL, "::ZZZZ", x, NULL);

// conjugate gradient minimization
conjgrad(x, 3*m.natoms, fret, mme, 0.1, 0.001, 2000 );

// Newton-Raphson minimization
newton( x, 3*m.natoms, fret, mme, mme2, 0.00000001, 0.0, 6 );

nmode(x, 3*m.natoms, mme2, 0, 0, 0.0, 0.0, 0 );
// mme2_timer();