As I recall, it does that when you only ask for a subset of the eigenvalues
and eigenvectors. Don't choose the method that allows you to stop
diagonalization after a small number of vectors have been found, and it
should compute the whole entropy term for you.
HTH,
Jason
On Tue, Jun 21, 2011 at 6:17 PM, Emmanuel Baribefe Naziga <
baribefe.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 22 2011 - 01:00:04 PDT
