[gmx-users] g_dist

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 1 01:23:10 CET 2012

On 1/02/2012 1:05 AM, dina dusti wrote:
> 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?

You've analyzed a data set with four distributions, but you'll have to 
go back to the column labels of dist.xvg to work out how to interpret 
the statistics of each distribution. It looks to me like your index 
groups are not the ones you thought they were.

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