[gmx-users] g_rdf (lyzozyme tutorial)

[Justin A. Lemkul]

On 6/12/12 7:24 AM, delara aghaie wrote:
> Dear Justin
> I use gromacs (4.0.5).
> This is the command line:
> g_rdf -f md_0_1.xtc -s md_0_1.tpr -xy -o rdf.xvg
>
> This is what appears on the screen and stops there without any change !!!
> ----------------------------------------------------------------------------------------------------------------------------
> Select a group: 3
> Selected 3: 'C-alpha'
> Select a group: 3
> Selected 3: 'C-alpha'
> Reading frame       0 time    0.000
> ---------------------------------------------------------------------------------------
> According to what you said I checked it for DPPC monolayer adsorbed on water
> surface. Again the same thing happened .........................
>
> This was the system that I have previously plotted so many rdf plots with -xy
> option for that. But that time the gromacs version was 3.3.3, something like this.
>
> So It seems there is something wrong with this gromacs version.
>

That's why I asked which version you were using.  This is a known bug that was 
introduced somewhere in the 4.0.x series, but was fixed in 4.0.7.  Upgrade and 
the problem will be solved.

-Justin

-- 
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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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