[gmx-users] g_order problems

[hseara at netscape.net]

Thank's a lot your quick replay, but I my case I have the following chains that contain insaturations:
 
-O-(O=)C-(CH2)7-CH=CH-(CH2)7-CH3
 
Can I still use g_order with the unsaturation??? Which is the first carbon I have to put in the index file the one in the ester or the first CH2? Its important the order of the carbons in the the index file? My molecule has two diferents chains, then I have to construct an index file for each or I can put all in the same file?
 
Thanks in advance Hector
 
-----Original Message-----
From: paloureiro at biof.ufrj.br
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wed, 16 Nov 2005 19:51:48 +0000
Subject: Re: [gmx-users] g_order problems



> As I understand for the explanation I only have to construct a index file
> containing "only" the groups containing in each, one of the carbons from
> which I want to get the order parameter.  Just as an example let's say a
> group that contains all my C33 carbons. Well I have done that but as well as
> in other posts I been looking the resulting outputs files are empty. For my
> surprise when I add more groups of carbons to analyze some outputs numbers
> are appearing, and I always get a number of values equal as number of groups
> - 2. What does it mean?? the connectivity is taken from the tpr file or it's
> using the order of the groups of the index file?? Sorry I'm quite confuse any
> help will be appreciated.
>  

Hi Hector,

if your chain goes from C1 to C15, for instance, then you must create an index 
file containing (only!) the following groups:

[ C1 ]
...
[ C2 ]
...
...
[ C15 ]
...

If there are 15 carbons, there will be 13 order parameters.

Regards.

Pedro.


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