[gmx-users] radius of gyration

[delara aghaie]

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?
-----------
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?

Thanks for your time
Regards
D.M




________________________________
 From: Justin A. Lemkul <jalemkul at vt.edu>
To: delara aghaie <d_aghaie at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, 11 June 2012, 17:21
Subject: Re: [gmx-users] radius of gyration
 


On 6/11/12 8:40 AM, delara aghaie wrote:
> Dear Justin.
> Thanks for your explanation.
> ............................................................
> In lyzozyme tutorial the radius of gyration has been plooted against simulation
> time (there 1000 ps).
> When I plot the same graph, the horizontal axis is up to 500 (The number of
> frames for data calculation).
> Although, the gyrate.xvg file has gyration data for these 500 frames, how can I
> tell gnuplot to plot gyration versus simulation time (1000 ps)?
> 

Are you talking about the tutorial or your own data?  If you are talking about the tutorial, then the run should have been for 1 ns.  If there are fewer frames, then either the .mdp file was changed to specify less time or the simulation stopped prematurely.

If you're talking about your own data, I have no way to know what was expected.  You can't plot more frames than are present.  I don't use gnuplot so I can't offer you any advice as to how you can manipulate the way the data are displayed.

-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

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