[gmx-users] Value output by g_energy

[Jackson Chief Elk]

I am testing for water located in the pore of cyclodextrin.  I am calculating the interaction energies for water-water, cyclodextrin-water using the programs located at;
https://github.com/jchiefelk/GROSOLLIG <https://github.com/jchiefelk/GROSOLLIG>
AND

https://github.com/jchiefelk/GROsoLEv4.5 <https://github.com/jchiefelk/GROsoLEv4.5>

The values I get make sense, and compare well to this paper;  
http://pubs.acs.org/doi/abs/10.1021/jp506716d <http://pubs.acs.org/doi/abs/10.1021/jp506716d>

I am just double checking that single pair interactions are calculated once, that question came up in group meeting today.  Thanks for your help.

Cheers,
Jackson


> On Nov 25, 2014, at 6:53 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 
> On Wed, Nov 26, 2014 at 1:01 AM, Jackson Chief Elk <jchiefelk at gmail.com>
> wrote:
> 
>> Is g_energy printing out the intermolecular energies for non redundant
>> pairs?
> 
> 
> g_energy doesn't print intermolecular energies, redundant or otherwise.
> 
> mdrun computes quantities for a single pair interaction once, because
> that's faster than the alternatives.
> 
>  Or does the energy need to be divided by a factor of 2?
>> 
> 
> What did your test with a sodium-chloride ion pair 1nm apart in vacuum tell
> you? :-)
> 
> Mark
> 
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