#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include <assert.h>
#include "nabcode.h"
extern char NAB_rsbuf[];
static int mytaskid, numtasks;

static MOLECULE_T *m;

static REAL_T xyz[4000], fret;

static FILE_T *file1;

int main( argc, argv )
	int	argc;
	char	*argv[];
{
	nabout = stdout; /*default*/

	mytaskid=0; numtasks=1;
static INT_T __it0001__;
static INT_T __it0002__;
static INT_T __it0003__;
static INT_T __it0004__;
static REAL_T __ft0001__;
static REAL_T __ft0002__;
file1 = fopen( "out.traj", "w" );

m = getpdb( "3jvs_wat_box.pdb", NULL );
readparm( m, "3jvs_wat_box.prmtop" );
mm_options( "cut=999., ntpr=50, ntwx=1, nsnb=99999, diel=C, gb=1, dielc=1.0 , wcons=10000" );
setxyz_from_mol(  &m, NULL, xyz );
mme_init( m, "::H*", "::!@H=", xyz, file1 );


conjgrad( xyz, ITEMP( __it0001__, 3 *  *( NAB_mri( m, "natoms" ) ) ),  &fret, mme, FTEMP( __ft0001__, 1.000000E-01 ), FTEMP( __ft0002__, 1.000000E-03 ), ITEMP( __it0002__, 200 ) );


mm_options( "ntpr=1" );
newton( xyz, ITEMP( __it0001__, 3 *  *( NAB_mri( m, "natoms" ) ) ),  &fret, mme, mme2, FTEMP( __ft0001__, 1.000000E-08 ), FTEMP( __ft0002__, 0.000000E+00 ), ITEMP( __it0002__, 50 ) );


nmode( xyz, ITEMP( __it0001__, 3 *  *( NAB_mri( m, "natoms" ) ) ), mme2, ITEMP( __it0002__, 0 ), ITEMP( __it0003__, 0 ), FTEMP( __ft0001__, 0.000000E+00 ), FTEMP( __ft0002__, 0.000000E+00 ), ITEMP( __it0004__, 0 ) );

fclose( file1 );


	exit( 0 );
}