[gmx-users] g_rdf (lyzozyme tutorial)

delara aghaie d_aghaie at yahoo.com
Tue Jun 12 13:24:18 CEST 2012

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.


 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: Tuesday, 12 June 2012, 15:45
Subject: Re: [gmx-users] g_rdf (lyzozyme tutorial)

On 6/12/12 5:16 AM, delara aghaie wrote:
> Dear Gromacs users
> Today I encountered a new error.
> I want to calculte RDF for my protein's (alpha-c) dissolved in water.
> when I use the command line:
> g_rdf -f traj.xtc -s topol.tpr -o rdf.xvg
> and I choose 3 for (C-alpha) for both the reference and target groups, every
> thing goes well and I will have the rdf plot.
> Now if I add option (-xy) to use the only x and y components, and then I choose
> my two groups, the program does not do anything and it stops !!
> This is right even for the lyzozyme protein in Justin's tutorial.

What version of Gromacs is this?  Does g_rdf simply stop, or does it produce an error?  Does it produce a segmentation fault?

Also note that the -xy option is much more useful for systems involving surfaces or membranes; I doubt it will be very informative for a system that tumbles in 3 dimensions.  Notwithstanding, if there's a bug it should be fixed, but it may not be critical.


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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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