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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