Google can be your friend here as can the basic AMBER tutorials (B0, B1)
[which should be completed and understood prior to running someone's
previously built production scripts to get some idea of the steps required
to do a successful setup, run and analyses]; however, as noted in a post
by Jason Swails from 2011, "I don't know if there is a file describing
each term definitively, but the names are defined to be as helpful as
possible...".
energies are in kcal/mol
TEMP temperature, K
PRESS pressure, Bar
Etot total energy (of entire system)
EKtot total kinetic energy
EPtot total potential energy
BOND total bond energy
ANGLE total angle energy
DIHED total dihedral energy
1-4 NB sum of the nonbonded (van der Waals) from 1,4 interactions
in dihedrals (first and 4th atom) (noting these may be
scaled, see: SCNB). Note that these are calculated
separately (hence reported separately) and also note that
1-1, 1-2, and 1-3 bonded interactions are omitted (i.e. the
nonbonds from an atom, bond or angle since they are
effectively included in bond/angle energies and we do not
have atom self energies)
1-4 EEL sum of the electrostatics from 1,4 interactions (noting
these may be scaled, see: SCEE)
VDWAALS total vdw energy (not including 1-4's)
EELEC total electrostatic (not including 1-4's)
EHBOND total h-bond term energy (normally zero with modern force
fields since -1/r**10, 1/r**-12 terms are often omitted)
RESTRAINT total restraint energy
EKCMT total kinetic energy center of mass translation
VIRIAL total virial energy
VOLUME total volume of the system
Density total density of the system
You can also read-up on MM-PBSA (mmpbsa.py) in the manual to better
understand some of the energy components and how to re-calculate them for
sub-parts of your system from generated MD trajectories...
As far as Rgyr, SASA, look at the analyses sections of the tutorials and
learn about CPPTRAJ for trajectory analysis.
--tec3
Dear Sir or Madam,
It’s my great honour to contact with you.
For my project, I want to obtain some information from trajectories or .out files, which are intramolecular potential energy of the solute, total potential energy of the solute, radius of gyration and solvent-accessible surface area, and also LJ potential and electrostatic components split from potential energy. Do you have any advice to deal with that?
What’s more, could you provide me with the instructions of the meanings of the parameters in the .out files? As shown below, what are the precise meanings of all those abbreviations? I know some of them are obvious but the others are not. And I’ve searched for this thing for a long time but still not found the answers satisfied…So I finally wrote this email and look forward to getting some hints from your side.
Thank you very much in advance!
Kind regards,
Zhonghua XIA • PhD Candidate
Institute of Structural Biology
Helmholtz Zentrum Muenchen
German Research Center for Environmental Health
Ingolstaedter Landstrasse 1
D-85764 Neuherberg, Germany
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