// Try some conjugate gradient minimization

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

// 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 f[ 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=15.0, rgbmax=15.0, ntpr=50, nsnb=25, gb=1, diel=C" );
mme_init(m, NULL, "::ZZZZ", x, NULL);

// Do some minimization

dgrad = 0.00001;
conjgrad(x, 3*m.natoms, fret, mme, dgrad, 1.0, 1000 );
putxv(  argv[2] + ".mc2.x", "bench minimization", m.natoms, 0.0, x, v );
mme_timer();