[gmx-users] g_dist

dina dusti dinadusti at yahoo.com
Tue Jan 31 15:05:24 CET 2012

Dear Gromacs specialists,

Can you help me about g_dist?
I have a micelle system, I want to obtain distance between center of mass of micelle with the last of carbon bounded to head group in surfactant. 

It should be near 2.2 but when I did   "g_dist -f md.xtc -s md.tpr -b 150000 -o dist.xvg" and then selected micelle and the last carbon bounded to head group, respectively , and  next did "g_analyze -f dist.xvg -av" it give me : 
                                      std. dev.    relative deviation of
                       standard       ---------   cumulants from those of
set      average       deviation      sqrt(n-1)   a Gaussian distribition
                                                      cum. 3   cum. 4
SS1   5.324286e-02   2.182349e-02   3.984406e-04       0.287    0.064
SS2  -2.000683e-04   3.327947e-02   6.075972e-04       0.045   -0.036
SS3  -6.405102e-04   3.270624e-02   5.971315e-04       0.001   -0.052
SS4  -2.777796e-04   3.366480e-02   6.146323e-04       0.016   -0.013

What should I do for obtain correct distance? 

Best Regards
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