Dear Amber User and Developer,
I read in Ambertools 13 reference manual, in chapter 8 cpptraj, page
277-278.
subchapter : Matrix and Vector Analysis.
One of the Analysis is Thermo.
It mention :
[thermo [outthermo <filename>]] Mass-weighted covariance (mwcovar)
matrix only. Calculate entropy, heat capacity, and internal
energy from the structure of a molecule (average
coordinates, see above) and its vibrational frequencies
using standard statistical mechanical formulas for an ideal
gas. Results are written to <filename> if specified,
otherwise results are written to STDOUT. Note that this
implicitly converts calculated eigenvalues to frequencies.
I am trying to get information of heat capacity and internal energy of my
structure of a molecule.
I use this scritp:
cpptraj my-parameter-top.prmtop << EOF
trajin my-trajcectory.mdcrd
matrix mwcovar name mwthermo byatom out mwthermo.dat
diagmatrix mwthermo out evecs-.dat vecs 0 thermo outthermo thermo-2-wat.dat
EOF
Then after this execute I got file : mwthermo.dat as an output (size : 2.2
GB). It is a big output file.
I am expected to get only some number that told me heat capacity, entropy
and internal energy of my molecule.
Would you give me some way how to use vector analysis Thermo.
Other question : Is there any detail example how to use PCA, vector
analysis with ptraj or cpptraj in AmberTools ? cause I'd like to know more.
Thank you very much.
Setyanto Tri Wahyudi
ITB Biokimia
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Received on Wed Apr 02 2014 - 23:00:02 PDT
