Hello, Thomas!
Thanks so much for your detailed explanation. That helps me a lot.
Nice weekends,
Zhonghua
> On 27. Jul 2018, at 22:37, Thomas Cheatham <tec3.utah.edu> wrote:
>
>
> 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.
>
> --tec3Dear 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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Received on Fri Aug 17 2018 - 06:30:05 PDT
