[gmx-users] The energy output code

[Mark Abraham]

Uwe Richter wrote:
> Hi,
> 
> I'd rather resort to the following.
> 
> Extract each single frame from your trajectory.
> Check whether your criteria for including certain atoms/indices are
> fulfilled.
> Create a separate index file for each frame.
> Recalculate the energy.
> 
> With some scripting ability this approach could be automatized easily.

Indeed. If you extra the single frames to a .gro or .pdb format to make
life easy for the script, remember to take enough precision from the
binary trajectory to the text gro/pdb so that your subsequent energy
calculations are not meaningfully dependent on your text precision.
Check the manpage of tpbconv for details about this.

Mark