Dear prof. Case, and Daniel Roe,
I am sorry if this email sent two times. I thought my email undelivered
since I got notification from postmaster (postmaster.gbaships.com) I don't
know why.
Thank's for the respond.
I just look into my outpur file thermo-2.dat and this is the contain of the
file :
======
*******************
- Thermochemistry -
*******************
temperature 298.150 kelvin
pressure 1.00000 atm
molecular mass (principal isotopes) 43349.19600 amu
principal moments of inertia (nuclei only) in amu-A**2:
10192003.92 11275397.53 12641992.89
rotational symmetry number 1
Warning-- assumption of classical behavior for rotation
may cause significant error
rotational temperatures (kelvin) 0.00000 0.00000 0.00000
zero point vibrational energy -1336561770.3 (joules/mol)
-319236.86933 (kcal/mol)
-509.0594837 (hartree/particle)
Warning-- 10249 vibrations have low frequencies and may represent hindered
internal rotations. The contributions printed below assume that
these
really are vibrations.
warning: setting vibrational entropy to zero for mode 13999 with vtemp =
-271964833.912749
warning: setting vibrational entropy to zero for mode 14000 with vtemp =
-206962223.144815
warning: setting vibrational entropy to zero for mode 14001 with vtemp =
-160303581.214612
warning: setting vibrational entropy to zero for mode 14002 with vtemp =
-93713731.426489
warning: setting vibrational entropy to zero for mode 14003 with vtemp =
-87684059.689750
warning: setting vibrational entropy to zero for mode 14004 with vtemp =
-79906661.448946
warning: setting vibrational entropy to zero for mode 14005 with vtemp =
-65836520.078644
warning: setting vibrational entropy to zero for mode 14006 with vtemp =
-63521944.525420
....
.
.
.
(there are almost 4000 line)
then continue with :
freq. E Cv S
cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
--------------------------------------------------------------------------------
Total 37868394.472 -nan 17156.722
translational 0.888 2.979 57.778
rotational 0.888 2.979 59.973
vibrational 37868392.696 -nan 17038.971
1 0.101 0.592 1.986 17.124
2 0.233 0.592 1.986 15.472
3 0.313 0.592 1.986 14.883
4 0.520 0.592 1.986 13.875
5 0.619 0.592 1.986 13.530
6 0.788 0.592 1.986 13.051
7 1.498 0.592 1.986 11.774
8 1.907 0.592 1.986 11.294
9 2.232 0.592 1.986 10.982
10 2.634 0.592 1.986 10.654
11 3.154 0.592 1.986 10.296
12 3.218 0.592 1.986 10.256
.
.
.(until ..
.
.
9994 2696.302 3.855 0.001 0.000
9995 2702.649 3.864 0.001 0.000
9996 2707.884 3.871 0.001 0.000
9997 2725.954 3.897 0.001 0.000
9998 2733.508 3.908 0.001 0.000
9999 2739.742 3.917 0.001 0.000
=====
I have a question about this,.
======
freq. E Cv S
cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
--------------------------------------------------------------------------------
Total 37868394.472 -nan 17156.722
translational 0.888 2.979 57.778
rotational 0.888 2.979 59.973
vibrational 37868392.696 -nan 17038.971
=======
The freq (cm**-1) is this a wave number ?
Then what is E (kcal/mol) ? is this the internal energy ?
the number 1 to 9999, I assume a number of my frame of of trajectory.
Why the Cv and Enthropy (S) was down to zero ?
Can we set the Temperature (298.15 K) and Pressure ? or it was extracted
from the trajectory ?
Dear Daniel Roe,
Yes it is "very" big output, I just select all atom of my protein include
with hydrogen, with total about 6000 atoms.
I'd like to know what is the my protein enthropy, Cv and Internal energy,
Should I calculate all atom or can I used Carbon Alpha only ?
Thanks for help.
I will re-calculate again since I did not make rms-fit. thanks to remind me.
On Thu, Apr 3, 2014 at 9:31 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Wed, Apr 2, 2014 at 9:10 PM, Setyanto Md <stwahyudi.md.gmail.com>
> wrote:
>
> >
> > Then after this execute I got file : mwthermo.dat as an output (size :
> 2.2
> > GB). It is a big output file.
> >
>
> That is a *very* big output file - how many atoms are you selecting? Be
> aware that you will need at least as many trajectory frames (and ideally
> more) as you have eigenvectors, otherwise 1 or more of your resulting
> eigenvalues will be zero, which may affect the quasiharmonic analysis in
> unexpected ways. Also, you should probably perform some sort of RMS-fit
> prior to calculation of the matrix to remove overall rotation/translation
> of your molecule (unless for some reason you want that reflected in the
> resulting matrix).
>
> -Dan
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 08 2014 - 08:00:03 PDT
