[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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120508/b9f73c1c/attachment.html>
More information about the gromacs.org_gmx-users
mailing list