[gmx-users] Re:Re: g_helixorient problem

[Dallas B. Warren]

Command lines that you use?  Contents of the index files?  Contents of the output files?

Catch ya,

Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University

A polar bear is a Cartesian bear that has undergone a polar transformation



-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of stefhoor
Sent: Wed 12/9/2009 1:44 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Re:Re: g_helixorient problem
 
> Stefan Hoorman wrote:
> > I am trying to analyse the tilt of my helix with g_helixorient, but all
> > analysis come back as a straight line in 0. I have supplied
> > g_helixorient with the index file containing all carbon alpha atoms of a
> > single helix but simply cannot obtain anything more than this zero line
> > graphic.
> > Some help on the matter would be great.
>
> Something's wrong, but we can't possibly tell what without a lot more
> information.
>
> Mark
>
>
Ok then. My system comprises of a helix of 30 residues inserted into a
membrane model DPPC. The protein was inserted aligned to the z axis, which
is the normal axis of the membrane. The simulation was carried out for 50ns
and the hole system is properly equilibrated. From visual inspection, it is
possible to see that the helix is tilted compared to the normal axis. For
the g_helixorient analysis, I have created an index file containing all the
alpha carbon atoms that constituted my helical domain and analysed the hole
trajectory with g_helixorient. The tilt.xvg and also the other outputs all
come out as a straight line parallel to x, and 0 in the y axis.
If there is any more information please tell me if you need any more
information.
Thank you

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