[gmx-users] problem with g_oder : file empty

[Justin A. Lemkul]

Thielges, Sabine wrote:
> Hi,
>  
> I have done a MD of a system GPCR/POPC, and I was trying to check my membrane with g_order. I made the index file like indicated in the web site using 
>  
> make_ndx -f md_0_10.tpr -o sn1.ndx
> 
>> 12 & a C15 | a C14 | a C6 | a C1 | a C2 | a C3 | a C5 | a C7 | a C4 | a C5 | a C7 | a C4 | a C8 | a C9 | a C10 | a C11 | a C12 | a C13 |

Each carbon atom must be considered in separate groups.  See, for example:

http://oldwiki.gromacs.org/index.php/g_order

<snip>

>  There no number. It is like nothing happen. I didn't had that issu for the rmsd
>  calculation or even density. I have a nice plot for both
>  

Because the index group is wrong.  See the above link and try again.

-Justin

>  Could somebody help me on that?
>  
>  thank you in advance
>  
>  Sabine
> 
> 
> Dr. THIELGES Sabine
> Associate Research Officer
> Conseil national de recherches du Canada - National Research Council 
> Institut de recherche en biotechnologie - Biotechnology Research Institute 
> 6100, avenue Royalmount,  Montréal, Québec, H4P 2R2 
> tél:   (514) 496-6255
> sabine.thielges at cnrc-nrc.gc.ca
> 
> 
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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