[gmx-users] dumping energies

Jochen Hub jhub at gwdg.de
Mon Apr 10 18:24:31 CEST 2006

Ryan Day wrote:

>I am trying to get the energies of individual waters in a trajectory. I
>am currently using an index file that defines each water individually,
>but, since I have ~9000 waters and can only define 254 energygrps at a
>time, this gets ugly quickly. I found some discussion in the list
>archices about possibly creating a module (g_strain) or adding an option
>to gmxdump that would allow energy dumps of all atoms or pairs. Has
>anything like this been developed? Or should I continue with my ugly hacks?
>Ryan Day
>Department of Physics
>Rensselaer Polytechnic Institute

When defining too many energy groups your edr files might become huge. 
Think of the number of possible interactions between 9000 groups:
9000*(9000-1)/2 times the number of types of interactions.

So probably you want to do several reruns (mdrun -rerun). For each 
rerun, you can define new energy groups (some water molecules in your case)
 and this way get reasonable statistics.


Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de

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