[gmx-users] how to calculate internal energy for energygroups?

[Allen Smith]

Any progress on this? (I note a prior discussion of the idea for a
"g_strain" program, under the subject line of "How to print out vdw-14
energy terms for each pair in minimization?") I have actually defined
energygrps for each charge group in each residue, via a script (which I will
forward if desired), via which (along with gmxdump) it appears possible to
get out coulomb and lennard-jones interactions (subdivided into 1-4 bonded
and short-range) between said energy groups - but gmxdump indicates that the
bond energy terms are still only present for the entire system. I'd like to
do something like putting a number proportional to the total energies (would
"Energy" or "Sum Energy" - for the final stage in a minimization - be more
appropriate?) into the temperature field of a PDB file. (I have also
considered the possibility of doing this with forces - I will try outputting
force terms seperately via mdrun -sepdvdl with my next minimization, and
will use mdrun -rerun -sepdvdl on earlier trajectory files if this is
helpful - but the summation of forces (e.g., an atom under vdw pressure from
"above" and "below") would appear likely to cancel out information of
interest.)

    Thanks,

    -Allen

P.S. In regard to my earlier thoughts on FFTW improvements - will try to
work on at some point, but am mainly working on Linux boxes at the moment so
this is less of a concern. I have also discovered exactly how fast GROMACS
is at doing minimization of even a well-solvated protein, which also
decreases this priority; very nice job, guys!

>        [gmx-users] how to calculate internal energy for energygroups?
>                                       
>   Marc Baaden [4]baaden at smplinux.de 
>   Tue Jan 23 14:40:38 CET 2007
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>>>> David van der Spoel said:
> >> Maybe we should go back one step. The reason this is not implemented is
> >> because we thought it would be unnecessary. In addition, if you would do
> >> it per residue how would you categorize e.g. the dihedral terms with one
> >> atom in one residue and three atoms in another? Of course you can define
> >> something, but what does it mean?
>
>
>Ok, first a general comment:
>
>I have used this in the past and found that the sum of all bonded energy
>terms for a given residue or for a subpart of a molecule is a good measure
>for the internal strain of that entity. Of course one may want to normalize
>this depending on what one wants to compare (per residue / per atom / per
>domain ...).
>
>I agree that the part of this entity that is connected to the rest of the
>molecule is ambiguous. I usually disregard all bonded terms that are not
>entirely contained within the selected atoms (the logic being that you can
>always make your selection bigger if you want).
>
>The problem that there might be with the way g_energy works at the moment
>is that I think g_energy tries to split the energy in parts so that by
>summing the parts you obtain the total sum again. That is you can't put
>an atom in two selections at the same time.
>
>
>For the specific case I want to use this now:
>
>In the system we are simulating we observe a specific pattern of contacts vs
>the residues of the macromolecule. We think that the origin for this lies in
>the balance of the different force-field terms for each residue. So I would
>like to make a plot of the interaction energies for each residue with the rest
>of the system split into electrostatic, van der Waals and bond/angle/dihedral
>contributions to see what the major contributions are and whether the pattern
>varies from residue to residue.
>
>I hope this does make sense and provides at least one reason to implement
>such a procedure.
>
>Marc
>--
> Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
> mailto:[11]baaden at smplinux.de      -      [12]http://www.baaden.ibpc.fr
> FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

-- 
Allen Smith                       http://cesario.rutgers.edu/easmith/
February 1, 2003                               Space Shuttle Columbia
Ad Astra Per Aspera                     To The Stars Through Asperity