[gmx-users] g_order in GMX4.05

[Justin A. Lemkul]

lammps lammps wrote:
> Hello everyone,
>  
> I use the g_order to get the order parameter of the tails( C1A, C2A, 
> C3A, C4A) of DPPC. The are 100 molecules of DPPC
>  
> 1. I use the make_ndx -f dppc.trr -n index to produce the index file.
>  
>  > a C1A
>  > a C2A
>  > a C3A
>  > a C4A
>  > del 0-3
>  
> Q_1: Is the method  right to produce the index file?

There is a how-to on the g_order page:

http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order

Your procedure seems like it might be right, but what are atoms C1A, C2A, etc? 
This isn't the numbering I'm used to.  What are groups 0-3?

>  
> Then there only four groups orderly named C1A, C2A, C3A, C4A in the 
> index file.
>  
> 2. I use the g_order -n index -s npt.tpr ... to get the order parameter. 
> However, there are lots of errors

Don't use "..." when posting a command.  Provide the whole command.

>  
> .........
> WARNING: distance between atoms 29777 and 29779 > 0.3 nm (0.897513). 
> Index file might be corrupt.
> WARNING: distance between atoms 29789 and 29791 > 0.3 nm (0.709495). 
> Index file might be corrupt.
> WARNING: distance between atoms 29801 and 29803 > 0.3 nm (0.692954). 
> Index file might be corrupt.
> WARNING: distance between atoms 29813 and 29815 > 0.3 nm (0.784918). 
> Index file might be corrupt.
> WARNING: distance between atoms 29825 and 29827 > 0.3 nm (0.839048). 
> Index file might be corrupt.
> WARNING: distance between atoms 29837 and 29839 > 0.3 nm (0.851105). 
> Index file might be corrupt.
> WARNING: distance between atoms 29849 and 29851 > 0.3 nm (0.790752). 
> Index file might be corrupt.
> WARNING: distance between atoms 29861 and 29863 > 0.3 nm (0.836583). 
> Index file might be corrupt.
> WARNING: distance between atoms 29873 and 29875 > 0.3 nm (0.854105). 
> Index file might be corrupt.
> WARNING: distance between atoms 29885 and 29887 > 0.3 nm (0.847901). 
> Index file might be corrupt.
> WARNING: distance between atoms 29897 and 29899 > 0.3 nm (0.758556). 
> Index file might be corrupt.
> ...........
>  
> Why?
>  

These messages seem to indicate that you have non-sequential carbon atoms. 
Cross-check the atom names you've used to create the index file with the actual 
coordinates.

-Justin

> 3. Result
>  
> Last frame          4 time  240.000  
> Read trajectory. Printing parameters to file
> Atom 1 Tensor: x=-0.267416 , y=-0.245994, z=0.51341
> Atom 2 Tensor: x=-0.207203 , y=-0.171233, z=0.378436
> Back Off! I just backed up order.xvg to ./#order.xvg.1#
> Back Off! I just backed up deuter.xvg to ./#deuter.xvg.1#
> gcq#51: "The Stingrays Must Be Fat This Year" (Red Hot Chili Peppers)
> [tianwd at localhost dppcden5]$ cat order.xvg
> # This file was created Sun Apr 23 10:10:35 2006
> # by the following command:
> # g_order -f traj.trr -n index.ndx -s npt.tpr -o -e 240
> #
> # g_order is part of G R O M A C S:
> #
> # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
> #
> @    title "Order tensor diagonal elements"
> @    xaxis  label "Atom"
> @    yaxis  label "S"
> @TYPE xy
>            1      -0.267416      -0.245994        0.51341
>            2      -0.207203      -0.171233       0.378436
> [tianwd at localhost dppcden5]$
> 
> 
> -- 
> wende
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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