[gmx-users] dumping energies

[Jochen Hub]

Ryan Day wrote:

>Hello,
>
>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?
>
>Thanks,
>
>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.

cheers,
jochen

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