[gmx-users] centre of the system: error

[Justin A. Lemkul]

minnale wrote:
>  
> Hi all,
> I am trying to make centre of the bilayer so I used following command line
> trjconv -f 20nspopc.xtc -centre rect -o 20nstrjout.xtc -n water.ndx 
> based on http://www.gromacs.org/pipermail/gmx-users/2003-June/005995.html
> here I selected 3 (solution) again 3 (solution) for output of the 
> selecting group
> this command ran fine
> when I feed 20nstrjout.xtc to g_density
> g_density -f 20nstrjout.xtc -s em.tpr -d z -o waterden -n water.ndx
> Group    0 (      System) has 14036 elements
> Group    1 (        POPC) has  6656 elements
> Group    2 (        SOL) has  7380 elements
> Group    3 (        SOL) has  7380 elements
> Select a group: 3
> Selected 3: 'SOL'
> Reading frame      0 time    0.000  Segmentation fault
> 
> where is the mistake happening?
> 

SOL is not "solution," it is "solvent," i.e. water.  If you want to center 
around the water, with the bilayer leaflets on opposite sides of the box, that's 
what you'll get.  If you want to center about POPC, then select POPC.

-Justin

> Could anyone tell me
> 
> Thanks in advance
> 
> 
> 
> ICL 
> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/2657076_2649302/2660191/1?PARTNER=3&OAS_QUERY=null>
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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