Dear Mark,
I am a bit confuse with yr advice,
after i did g_gyrate, I examine the gyration.xvg and I get this( I only show
part of the data):
@ title "Radius of gyration"
@ xaxis label "Time (ps)"
@ yaxis label "Rg (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Rg"
@ s1 legend "RgX"
@ s2 legend "RgY"
@ s3 legend "RgZ"
0 0.101214 0.0862465 0.0765928 0.0758378
10 0.10097 0.0852172 0.0766285 0.0764949
20 0.101094 0.0841315 0.0759198 0.0780227
30 0.101178 0.0845673 0.0760734 0.0780282
40 0.101101 0.0855135 0.0761306 0.0765843
50 0.102186 0.086539 0.0774698 0.077009
60 0.102582 0.0867398 0.0774364 0.0776702
70 0.103084 0.0862637 0.0772064 0.0798831
80 0.10225 0.0851082 0.0779015 0.0786001
90 0.101688 0.0866644 0.0763416 0.0771902
100 0.101904 0.0851727 0.0768526 0.0786537
and the g_analyze for thr gyration.xvg is as follow:
Read 4 sets of 201 points, dt = 10
std. dev. relative deviation of
standard --------- cumulants from those of
set average deviation sqrt(n-1) a Gaussian distribition
cum. 3 cum. 4
SS1 1.038435e-01 1.336665e-03 9.451647e-05 0.110 -0.213
SS2 8.344679e-02 1.333312e-03 9.427939e-05 -0.028 -0.097
SS3 8.096852e-02 1.840205e-03 1.301221e-04 -0.254 -0.037
SS4 nan nan nan nan nan
is it the average set SS1 (1.038435e-01) is the average of the 1st column for
the data in gyration.xvg?
Sorry for all the trouble.
thanks
--- On Mon, 11/24/08, Mark Abraham <[EMAIL PROTECTED]> wrote:
> From: Mark Abraham <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] average radius of gyration
> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
> Date: Monday, November 24, 2008, 12:19 PM
> Q. Y. HUAN wrote:
> > Dear all,
> > I did g_gyrate and I obtained a gyration graph, then i
> did g_analyze with the following command: g_analyze -f
> gyration.xvg -av
> > Then I obtained a set of values as follow:
> >
> > Read 4 sets of 201 points, dt = 10
> >
> > std. dev.
> relative deviation of
> > standard ---------
> cumulants from those of
> > set average deviation sqrt(n-1) a
> Gaussian distribition
> >
> cum. 3 cum. 4
> > SS1 1.118544e+06 4.723966e+04 3.340348e+03
> 0.279 -0.187
> > SS2 7.170712e+05 3.874540e+04 2.739714e+03
> 0.144 0.006
> > SS3 6.360595e+05 3.469453e+04 2.453274e+03
> 0.457 -0.011
> > SS4 5.754301e+05 2.800850e+04 1.980500e+03
> -0.060 -0.172
> >
> >
> > So, my question is, is it I sum up all the 4 set of
> average value and divide by 4 and the answer will be my
> final average value of gyration?
>
> Start by reading g_gyrate -h, then examine your
> gyration.xvg
>
> Mark
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