[gmx-users] non-bonded interactions energies

[Naomi Fox]

On Fri, Jan 27, 2012 at 12:22 PM, Justin A. Lemkul <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 <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"

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.
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