[gmx-users] radius of gyration

[Justin A. Lemkul]

On 6/11/12 9:28 AM, delara aghaie wrote:
> Dear Justin
> Thanks again. Ok I got it.
> Only there remains a question:
> you mean it is possible that the simulation has finished for 1 ns but the .xtc
> file does not have the information for whole frames or even it is possible for
> g_gyrate program to crash and give the non-compelete .xvg file?
>

A large number of things are possible.  You can use gmxcheck to verify the 
integrity of the .xtc file, and inspect the .log file to make sure the 
simulation was conducted as you expect it to.  If g_gyrate had crashed, it would 
have been fairly obvious in the terminal.

-Justin

> 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, 17:46
> *Subject:* Re: [gmx-users] radius of gyration
>
>
>
> 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
>
> ========================================
>
>
>
>
>
>

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

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

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