[gmx-developers] 6-12 and coulomb / energy / atom pairs

[Anton Feenstra]

marcos lourenzoni wrote:

> Dear Gromacs Developers,
> 
> 
> I need evaluate the resulting (6-12 and coulomb) energy of the each atom of protein.
> The energy must be intra and intermolecular. 
> Example: 
> The total number of protein atoms is: (natom)
> The total number of protein atoms is: (nwater)
> I need natom*nwater energy values of every simulation dt.
> Another case.
> I need natom*(natom-1) energies values.

You're talking huge numbers of energy values. (e.g. 1000 atoms in the (small)
protein, and 2000 in the water, already makes 2x1000x2000 = 4e6!) All these
energies are calculated in mdrun, but only totals for groups of atoms (default
for the whole system) are stored in the energy file (.edr). Without modifying
the source code, you cannot get them out in any easy way.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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