[gmx-users] average radius of gyration

[Q. Y. HUAN]

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 <Mark.Abraham at anu.edu.au> wrote:

> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] average radius of gyration
> To: "Discussion list for GROMACS users" <gmx-users at 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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