[gmx-users] non-bonded interactions energies

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 27 21:22:09 CET 2012

Naomi Fox wrote:
> On Thu, Jan 26, 2012 at 7:20 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     On 27/01/2012 12:35 PM, Naomi Fox wrote:
>         I would like to print out a list of non-bonded interactions and
>         their associated LJ-potentials and coulombic potentials.
>         I tried g_energy, but couldn't figure out the combination of
>         parameters to get this information.
>     During the simulation, you can only save the magnitude of the
>     interactions between energy groups (see manual), and by default the
>     only such group is the whole system. mdrun -rerun is useful for
>     re-computing quantities based on an existing simulation.
>     Mark
> So what you're saying is it isn't possible?  
> When I rerun mdrun with the -seppot option, I see in the md.log file 
> that I get the VdW and Coulomb V and dVdl for node 0 (the only node).
> There is no way to print the exact contribution from each individual 
> interaction?

It certainly is possible, you just need to specify energygrps (in the .mdp file) 
for the interactions you want to monitor, as Mark said.  The -seppot flag is for 
the free energy code, IIRC, not a magic option to dump a bunch of different 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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