On Thu, Sep 20, 2012 at 9:17 AM, Sangmin Lee <dadu0413.yonsei.ac.kr> wrote:
> Dear all developers and users.
>
> I use Amber11 and Ambertools1.4 based on cygwin. In Ambertools, I have
> simulated normal mode calculation using NAB. Under the same conditions, I
> have conducted nmode calculation using MMPBSA.py. When I compared obtained
> two types of energy, these are not matched.
>
> (1) What reason does not match?
>
You do not appear to be using the same minimization routine (or for the
same number of steps), so your starting snapshot will almost certainly be
different than the one used by MMPBSA.py (which can significantly affect
your results).
Also, your potential parameters (e.g., rgbmax) are different in your
program as compared to MMPBSA.py.
>result(MMPBSA.py)
>
>
>
> NMODE Calc
> iter Total bad vdW elect nonpolar genBorn
> frms
> ff: 1 98.67 16.89 -0.48 139.08 0.00 -56.82
> 1.66e-02
> Energy = 9.8673201693e+01
> RMS gradient = 1.6578972407e-02
> dysev time = 0.00 seconds
>
> - Thermochemistry -
> Temperature: 298.150
> Pressure: 1.000
> Mass: 342.296
> Principal moments of inertia in amu-A**2:
> 1254.93 3540.35 4195.41
> Rotational symmetry number is 1
> Assuming classical behavior for rotation
> Rotational temperatures: 0.019 0.007 0.006
> found 3 imaginary frequencies
> Zero-point vibrational energy: 229.041
> freq. E Cv S
> cm**-1 kcal/mol cal/mol-K cal/mol-K
> Total: 341.923 88.733 152.499
> translational: 0.888 2.979 43.357
> rotational: 0.888 2.979 35.071
> vibrational: 241.474 82.775 74.072
> ff energy: 98.673
> 1 -2.453
> 2 -1.584
> 3 -1.359
> 4 -0.000
> 5 0.000
> 6 0.000
> 7 15.668
> 8 28.271
> 9 33.396
> 10 54.572 0.596 1.974 4.640
> 11 74.358 0.598 1.965 4.030
>
>
>
> >result(NAB)
>
> NMODE Calc
> iter Total bad vdW elect nonpolar genBorn
> frms
> ff: 1 98.67 16.89 -0.48 139.08 0.00 -56.82
> 1.66e-02
> Energy = 9.8673201693e+01
> RMS gradient = 1.6578972407e-02
> dysev time = 0.00 seconds
>
> - Thermochemistry -
> Temperature: 298.150
> Pressure: 1.000
> Mass: 342.296
> Principal moments of inertia in amu-A**2:
> 1254.93 3540.35 4195.41
> Rotational symmetry number is 1
> Assuming classical behavior for rotation
> Rotational temperatures: 0.019 0.007 0.006
> found 3 imaginary frequencies
> Zero-point vibrational energy: 229.041
> freq. E Cv S
> cm**-1 kcal/mol cal/mol-K cal/mol-K
> Total: 341.923 88.733 152.499
> translational: 0.888 2.979 43.357
> rotational: 0.888 2.979 35.071
> vibrational: 241.474 82.775 74.072
>
These look the same to me... What am I missing? (Comparing the
"vibrational" line to the output you pasted above...
(2) And what is the reason for the different Default of mm_options of
> MMPBSA.py and NAB? Especially why the default value of dielectric
> constant(dielc)is 4.0 and how to control rgbmaxin MMPBSA.py?
>
We tried to be consistent with the original Nmode functionality in
mm_pbsa.pl, so we copied those defaults. To change the mm_options of
nmode, go to line 530 of
$AMBERHOME/AmberTools/src/mmpbsa_py/MMPBSA_mods/calculation.py and change
the 'option_string' to whatever mm_options you want.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 20 2012 - 07:00:03 PDT
