[gmx-users] g_dist

[Mark Abraham]

On 1/02/2012 4:26 PM, dina dusti wrote:
> Dear Prof.
>
> Thank you very much from your response.
> Yes, dist.xvg has four column consists origin distance and distances 
> in direction x, y , z. So distance that I want according to result of 
> g_analyze, is 5.324286e-02 that isn't correct. I selected 2 groups, 
> micelle and the last carbon bounded with head group for index file.
> Also, I did this job for micelle and head group, and micelle with 
> other groups but my results (distances) were all of them near the zero.
> Please help me to obtain correct distance.
>

If your groups are correct and g_dist is correct and your simulation 
conforms to your expectation of micelle structure then at least one of 
the foregoing isn't true. You may have a periodicity artefact (see 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions 
for how to avoid if so). You may have no micelle. Your groups may be wrong.

Mark
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