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On 1/02/2012 4:26 PM, dina dusti wrote:
<blockquote
cite="mid:1328073973.20042.YahooMailNeo@web121304.mail.ne1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:times
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<div>Dear Prof.</div>
<div><br>
</div>
<div>Thank you very much from your response. <br>
</div>
<div>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.</div>
<div>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.</div>
<div>Please help me to obtain correct distance.</div>
<br>
</div>
</blockquote>
<br>
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 <a
href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a>
for how to avoid if so). You may have no micelle. Your groups may be
wrong.<br>
<br>
Mark<br>
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