[gmx-users] g_dist

[Mark Abraham]

On 3/02/2012 3:17 AM, dina dusti wrote:
> Dear Prof
>
> Thank you very much from your response.
> She said me:
> "In g_dist, when you select two groups for distance calculation, it 
> computes the distance between COM's of groups. Now, what is expected 
> for the distance between the micelle's COM and the COM of (e.g.) head 
> groups? Clearly, it's near zero ! So you should first calculate the 
> distance for each group separately and then average over all distances."
>
> But I didn't understand what was her mean about "you should first 
> calculate the distance for each group separately and then average over 
> all distances.", because I did g_dist between micelle and for example 
> head group and then used g_analyze for dist.xvg and I had the quantity 
> near zero!!!
>

This can be done more efficiently with g_bond, treating each 
head-to-tail distance as a "bond".

Mark
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