[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.
> 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.
> 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
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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