Hello ,
I am getting the following output from NAB for normal mode calculations. It
prints just the frequencies with no other thermodynamic data.
Energy = 7.0235230090e+02
RMS gradient = 8.9254780771e-08
Order of the Hessian matrix 3672
Number of eigenvalues and eigenvectors sought 20
Number of Arnoldi vectors 40
Convergence achieved after 61 iterations
- Thermochemistry -
Temperature: 298.150
Pressure: 1.000
Mass: 9195.156
Principal moments of inertia in amu-A**2:
306533.05 2908243.03 2916073.81
Vibrational frequencies in cm**-1
1 0.00001
2 0.00003
3 0.00003
4 0.00049
5 0.00052
6 0.00160
7 1.09146
8 1.28574
I used the following NAB script
molecule m;
int ier;
float m_xyz[dynamic], f_xyz[dynamic];
float dgrad, fret;
m = getpdb("coordinate.pdb");
allocate m_xyz[3*m.natoms];
allocate f_xyz[3*m.natoms];
readparm(m, "topology.top");
mm_options("rgbmax=100., cut=999.0, ntpr=50, nsnb=99999, gb=1, diel=C,
dielc=4");
mme_init(m, NULL, "::ZZZZ", m_xyz, NULL);
// Do some conjugate gradients.
dgrad = 0.001;
setxyz_from_mol( m, NULL, m_xyz );
ier = conjgrad(m_xyz, 3*m.natoms, fret, mme, dgrad, 1.0, 50000);
// Do some Newton-Raphson.
mm_options("ntpr=1");
dgrad = 1.e-7;
ier = newton(m_xyz, 3*m.natoms, fret, mme,mme2, dgrad, 0.0, 15);
// get the normal modes:
ier = nmode( m_xyz, 3*m.natoms,mme2, 500,2,0.0,0.0,0);
What could be wrong?
Thanks.
Emmanuel
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Received on Tue Jun 21 2011 - 17:30:03 PDT
