Thanks David and Jason. I have all the output now. I have another question
though. Is there a way to know if SCEE and SCNB sections are read from the
topology file in this calculation?
Thanks.
Emmanuel.
On Wed, Jun 22, 2011 at 6:05 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Jun 21, 2011, Emmanuel Baribefe Naziga wrote:
> >
> > I am getting the following output from NAB for normal mode calculations.
> It
> > prints just the frequencies with no other thermodynamic data.
> >
> > 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
> >
> >
> > mm_options("rgbmax=100., cut=999.0, ntpr=50, nsnb=99999, gb=1, diel=C,
> > dielc=4");
>
> Don't do this! The "dielc" parameter should not be used in conjunction
> with
> gb. (The manual just says this parameter is for "non-gb" calcualations;
> I'll
> update it to add a warning about not using it with gb.) You are
> effectively
> screening charge-charge interactions twice.
>
> >
> > // get the normal modes:
> > ier = nmode( m_xyz, 3*m.natoms,mme2, 500,2,0.0,0.0,0);
>
> You should not set ntrun=2 here. It is computing the lowest two non-zero
> frequencies, then quitting. Thermodynamics can only be computed if all the
> eigenvalues are determined, so use ntrun=0 or 1.
>
> ....dac
>
>
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Received on Wed Jun 22 2011 - 08:30:04 PDT
