[gmx-users] non-bonded interactions energies

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 27 22:22:19 CET 2012

Naomi Fox wrote:
> On Fri, Jan 27, 2012 at 12:22 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>     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>
>         <mailto: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 interactions.
>     -Justin
> Thanks Mark and Justin.
> Two more questions:
> 1) How do I define an energy group for an interaction?  All I found for 
> examples in the manual are "Protein" and "SOL"

You can define any group you wish with a suitable index group.

> 2) Can I dump all the interactions listed as [ pairs ] in the .top file? 
>  I only need them for a single conformation and not for a full trajectory. 

Pair interactions are fixed quantities so they can be calculated by hand (or by 
a script, likely preferrable), otherwise you can set them as energygrps as well 
(one-atom groups).



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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