[gmx-users] Calculating intermolecular energies of water

[Mark Abraham]

On Tue, Oct 28, 2014 at 6:27 PM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> On 2014-10-28 18:12, Jackson Chief Elk wrote:
>
>> Hi,
>> When using g_energy to calculate short-range Coulomb interactions between
>> a dynamically sized group of water, made with g_select, does the output
>> contain both bonded and non bonded contributions?
>> Jackson
>>
>>  I don't think this is possible at all. You need to define energy groups
> before your simulation.


Indeed. But if Jackson meant to ask about short-range Coulomb, then bonded
contributions do not apply. Nor would they if the water model was rigid, as
is typically the case.

Mark


>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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