// carry out molecular mechanics minimization and some simple dynamics
molecule m, mi;
int  ier;
float  m_xyz[ dynamic ], f_xyz[ dynamic ], v[ dynamic ];
float  dgrad, fret, dummy[2];

mi = bdna( "gcgc" );
putpdb( mi, "temp.pdb" );
m = getpdb_prm( "temp.pdb", "leaprc.ff94", "", 0 );

allocate m_xyz[ 3*m.natoms ];  allocate f_xyz[ 3*m.natoms ];
allocate v[ 3*m.natoms ];
setxyz_from_mol( m, NULL, m_xyz );

mm_options( "cut=25.0, ntpr=10, nsnb=999, gamma_ln=5.0" );
mme_init( m, NULL, "::ZZZ", dummy, NULL );
fret = mme( m_xyz, f_xyz, 1 );
printf( "Initial energy is %8.3f\n", fret );

dgrad = 0.1;
ier = conjgrad( m_xyz, 3*m.natoms, fret, mme, dgrad, 10.0, 100 );
setmol_from_xyz( m, NULL, m_xyz );                                     
putpdb( "gcgc.min.pdb", m );                                           

mm_options( "tautp=0.4, temp0=100.0, ntpr_md=10, tempi=50." );         
md( 3*m.natoms, 1000, m_xyz, f_xyz, v, mme );                             
setmol_from_xyz( m, NULL, m_xyz );                                     
putpdb( "gcgc.md.pdb", m );