[gmx-users] g_bundle!

[priyanka srivastava]

Does this mean defining my own .ndx file and not using
the default one?

If yes, can you please drop some hints of how to make
the .ndx file for this purpose. 

thanks and regards,
Pri...


--- Alan Dodd <anoddlad at yahoo.com> wrote:

> I've used g_bundle a lot for just this sort of
> thing.  You need to define the top and bottom of the
> helix as seperate groups, and define them *very*
> carefully - it does make a difference how you do it,
> presumably because g_bundle just plots the axis
> between the COM of both groups?  I usually define as
> close to 1 complete turn of the backbone of the
> helix at each end as possible.
> Your output is not surprising, given what you've
> asked the program for - the axis between two points
> that precisely overlap ;-)
> 
> ----- Original Message ----
> From: priyanka srivastava <priyankaps4 at yahoo.com>
> To: gmx-users at gromacs.org
> Sent: Wednesday, June 20, 2007 3:27:42 PM
> Subject: [gmx-users] g_bundle!
> 
> 
> Dear All,
> 
> I want to calculate tilt angle of a peptide inserted
> inside the lipid bilayer (i.e. angle between the
> helical axis and bilayer normal). From previous
> posts
> I got an idea that g_bundle wud solve my problem.
> 
> I am issuing the following on the command line:
> 
> g_bundle -f test.xtc -s test.tpr -na 2 -z -tu ps
> 
> This asks me to "Select a group of top and a group
> of
> bottom atoms"
> 
> Group     0 (      System) has 12877 elements
> Group     1 (     Protein) has   102 elements
> Group     2 (   Protein-H) has    79 elements
> Group     3 (     C-alpha) has    10 elements
> Group     4 (    Backbone) has    31 elements
> Group     5 (   MainChain) has    41 elements
> Group     6 (MainChain+Cb) has    49 elements
> Group     7 ( MainChain+H) has    54 elements
> Group     8 (   SideChain) has    48 elements
> Group     9 ( SideChain-H) has    38 elements
> Group    10 ( Prot-Masses) has   102 elements
> 
> when I chose "1" and "1" it gives all angles as 90,
> which is wrong and bun_tiltr is reported as "nan".
> The
> manual says that "the program reads two index groups
> and divides both of them in -na parts".
> I am a lil confused! what should be my choice here?
> 
> regards,
> Pri...
> 
> 
> 
> 
>        
>
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