[gmx-users] how to extract the potential energy of the molecule

[Anton Feenstra]

David van der Spoel wrote:
> On Fri, 2003-03-21 at 07:57, Liu Songbai wrote:
> 
>>hi,all
>>     After completion of molecular dynamics simulation of a molecule 
>>solvated in water, I used "g_energy" to extract the potential energy of the 
>>pharmaceutical molecule because two energy groups, the molecule and water, 
>>were used in the simulation. But there was only one potential option which 
>>is  total potential energy of system I think, I want only the solvate 
>>potential not the total. How to obtain the individual potential energy? any 
>>suggestions?
>>
> 
> Something must have gone wrong when running grompp. Run it again and
> check the output on the screen, it will state which energy groups you
> have.

Maybe Liu is confused by the naming of the energy groups. The potential
energy you (Liu) mention, is the total energy. But all other contributions
are (or, should) be also listed, as separate components for solute-solute,
solute-solvent and solvent-solvent, and for 'LJ', 'Coul' and several
other flavors of energy classes used in Gromacs. You'll have to add
several of those terms together to get the numbers you are looking for.


-- 
Groetjes,

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