# [gmx-users] radius of gyration

dina dusti dinadusti at yahoo.com
Tue May 8 19:06:55 CEST 2012

```Dear GROMACS Specialists,

I have one question about radius of gyration for micelle, Please help me.
My micelle is created at 100000 ps by Martini CG force field.
When I calculate the radius of gyration from this time as "g_gyrate -f 1.xtc -s 1.tpr -n 1.ndx -o gyrate.xvg -b 100000" and "g_analyze -f gyrate.xvg -av -ee", my answer is:

std. dev.    relative deviation of
standard       ---------   cumulants from those of
set      average       deviation      sqrt(n-1)   a Gaussian distribition
cum. 3   cum. 4
SS1   1.811581e+00   1.586248e-02   3.708049e-05       0.399    0.318
SS2   1.476027e+00   5.355297e-02   1.251867e-04       0.009   -0.039
SS3   1.480446e+00   5.226397e-02   1.221735e-04       0.004   -0.060
SS4   1.478287e+00   5.332558e-02   1.246551e-04      -0.005   -0.084

Set   1:  err.est. 0.000281889  a 0.468124  tau1 20.1606  tau2 308.225
Set   2:  err.est. 0.0024333  a 0.925872  tau1 536.208  tau2 8592.94
Set   3:  err.est. 0.00190226  a 0.971916  tau1 544.756  tau2 7044.58
Set   4:  err.est. 0.00267771  a 0.991392  tau1 629.613  tau2 88302

But when I calculate it from start time of simulation as "g_gyrate -f 1.xtc -s 1.tpr -n 1.ndx -o gyrate.xvg" and "g_analyze -f gyrate.xvg -av -ee", my answer is:

std. dev.    relative deviation of
standard       ---------   cumulants from those of
set      average       deviation      sqrt(n-1)   a Gaussian distribition
cum. 3   cum. 4
SS1   1.979407e+00   6.228274e-01   1.392685e-03       2.317    4.169
SS2   1.613785e+00   5.401095e-01   1.207722e-03       2.478    4.949
SS3   1.601265e+00   4.713569e-01   1.053986e-03       2.547    5.460
SS4   1.624623e+00   5.387790e-01   1.204746e-03       2.208    3.719

Warning: tau2 is longer than the length of the data (1.2e+06)
the statistics might be bad
invalid fit:  e.e. -nan  a 5.56656  tau1 674505  tau2 8.75077e+07
Will fix tau2 at the total time: 1.2e+06
a fitted parameter is negative
invalid fit:  e.e. -nan  a 18.789  tau1 806548  tau2 1.2e+06
Will use a single exponential fit for set 1
Set   1:  err.est. 0.212562  a 1  tau1 69885.8  tau2 0
a fitted parameter is negative
invalid fit:  e.e. 20.1017  a 2.22647  tau1 210523  tau2 -6.77257e+08
Will fix tau2 at the total time: 1.2e+06
a fitted parameter is negative
invalid fit:  e.e. -nan  a 3.04296  tau1 249121  tau2 1.2e+06
Will use a single exponential fit for set 2
Set   2:  err.est. 0.170009  a 1  tau1 59447.7  tau2 0
a fitted parameter is negative
invalid fit:  e.e. 0.139564  a 1.61177  tau1 36947.7  tau2 11359.6
Will fix tau2 at the total time: 1.2e+06
a fitted parameter is negative
invalid fit:  e.e. -nan  a 2.35981  tau1 195092  tau2 1.2e+06
Will use a single exponential fit for set 3
Set   3:  err.est. 0.149959  a 1  tau1 60729.6  tau2 0
a fitted parameter is negative
invalid fit:  e.e. 6.4854  a 5.92085  tau1 759910  tau2 -1.67528e+07
Will fix tau2 at the total time: 1.2e+06
a fitted parameter is negative
invalid fit:  e.e. -nan  a 30.0389  tau1 922726  tau2 1.2e+06
Will use a single exponential fit for set 4
Set   4:  err.est. 0.184771  a 1  tau1 70566.6  tau2 0

and my plot of errest.xvg in the first one is similar with article "B. Hess, J. Chem. Phys. 116:209-217, 2002" but in the second one is different whereas err.est in second are similar to micellar articles.

I don't know which one is true, time of simulation start or time of creation of micelle?

Both of them (the radius of gyration) is in agreement with experimental but second one is more near than first one.

Please help me.
Thank you very much in advance.
Best Regards
Dina
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