I am using nmode to find a transition state structure(coordinates) and the
energy barrier between my input structure or mininum structure and that of
the transition state. My input structure has 24.0 kcal/mol of energy. The
output file I am looking at has as its last part for the transition state
search as :
step = 56
F = -0.488232E+01 GRDMAX = 0.662498E-03 GNORM = 0.132406E-03
E-NONB E-ELE E-HBOND E-BOND
-0.20634E+01 -0.28338E+02 0.00000E+00
0.57860E+00
E-ANGLE E-DIHED E-NB14 E-EEL14
0.27568E+01 0.45998E+01 0.57571E+01
0.11826E+02
E-POL E-3BOD
0.00000E+00 0.00000E+00
Found transition state:
***************** ***************** *****************
step = 56
F = -0.488232E+01 GRDMAX = 0.662498E-03 GNORM = 0.132406E-03
E-NONB E-ELE E-HBOND E-BOND
-0.20634E+01 -0.28338E+02 0.00000E+00
0.57860E+00
E-ANGLE E-DIHED E-NB14 E-EEL14
0.27568E+01 0.45998E+01 0.57571E+01
0.11826E+02
E-POL E-3BOD
0.00000E+00 0.00000E+00
b1 = -0.07361 b2 = 0.06656 tlamba = -0.17361
rms of step length = 0.0577350278
ene .step k-1 = -4.882317 ene .k = 14.533882
ene .step k-1 = -4.882317 ene .k = 7.543089
ene .step k-1 = -4.882317 ene .k = 3.070845
ene .step k-1 = -4.882317 ene .k = 0.208641
ene .step k-1 = -4.882317 ene .k = -1.623461
ene .step k-1 = -4.882317 ene .k = -2.796260
ene .step k-1 = -4.882317 ene .k = -3.547019
ene .step k-1 = -4.882317 ene .k = -4.027604
ene .step k-1 = -4.882317 ene .k = -4.335235
ene .step k-1 = -4.882317 ene .k = -4.532149
ene .step k-1 = -4.882317 ene .k = -4.658191
Coordinate origin is now the molecular center of mass
b1 = 0.00151 b2 = 0.02023 tlamba = -0.09849
rms of step length = 0.4152882440
ene .step k-1 = -4.658191 ene .k = 58.765594
ene .step k-1 = -4.658191 ene .k = 34.889225
ene .step k-1 = -4.658191 ene .k = 19.807583
ene .step k-1 = -4.658191 ene .k = 10.320876
ene .step k-1 = -4.658191 ene .k = 4.384055
ene .step k-1 = -4.658191 ene .k = 0.693016
ene .step k-1 = -4.658191 ene .k = -1.582165
ene .step k-1 = -4.658191 ene .k = -2.968536
ene .step k-1 = -4.658191 ene .k = -3.799999
ene .step k-1 = -4.658191 ene .k = -4.287485
ene .step k-1 = -4.658191 ene .k = -4.563759
***************** ***************** *****************
I hope this helps.
Thanks.
On Wed, 9 Jun 2004, David A. Case wrote:
> On Wed, Jun 09, 2004, Johnson Agbo wrote:
>
>> How is the output file for the transition state interpreted. I cannot
>> locate the barrier height from the results of the output file.
>
> Can you be more specific about what sort of output you are looking at? Is
> this from nmode? Maybe you could post a bit of the output that you find
> hard to interpret, plus a little bit about what you are doing.
>
> ...dac
>
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Received on Thu Jun 10 2004 - 01:53:00 PDT
