[gmx-users] radius of gyration

[Justin A. Lemkul]

On 6/11/12 9:09 AM, delara aghaie wrote:
> Dear Justin
> My question can be related to both. Ok let me talk about the tutorial. The
> simulation has finished compeletly and log file and other outputs show the
> completion of 1 ns simulation.
>
> this is part of gyrate.xvg file I see:
> -------------
> @ s0 legend "Rg"
> @ s1 legend "RgX"
> @ s2 legend "RgY"
> @ s3 legend "RgZ"
>           0     1.40391     1.20269     1.02309     1.20363
>           2     1.41596     1.21322     1.03459     1.21146
>           4 1.41283     1.21881     1.02271     1.20861
>           6     1.41882     1.21595     1.03424      1.2157
>           8      1.4139     1.20694     1.03791     1.21006
>          10     1.42295     1.21367     1.03899     1.22356
>          12     1.42184     1.20803      1.0391     1.22646
> ----
> ---
>       518     1.41756 1.20547     1.04411     1.21475
>         520     1.42478     1.21366     1.04952     1.21882
>         522     1.41129     1.20451     1.04001     1.20458
>         524     1.42205     1.20918     1.04929     1.21711
>         526     1.41778     1.20381     1.04779     1.21375
>         528     1.41853     1.20465     1.06006 1.20398
>         530     1.42129     1.20401     1.05779     1.21307
>                                                                288,8         Bot
> ---------------------------------------
> This was the start and end of data reported in gyrate.xvg file.
> all the outputs are written in files every 1000 steps (1000*0.002=2ps).
> I expect to see in gyrate.xvg file, the last line for 500 which corresponds to
> the (500*2=1000ps)
>
> can you please explain the result for having lines till 530?

Your output file is not labeled according to frame number, it is labeled 
according to time and thus 530 corresponds to the time of 530 ps.  If the file 
does indeed end there then either there is a corruption in the .xtc file, your 
simulation did not go to 1 ns, or g_gyrate exited prematurely.  It's up to you 
to figure out what may have gone wrong.  No one else can possibly know that.

> -----------
> About plotting the graph if I know use the two first coloumns, I will not have
> graph for Rg versus simulation time which I am interested in?
>

That's precisely what you will have.  Look at the data labels in the .xvg file 
and you will see what each data set is.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================