[gmx-users] Rv: g_helixorient question

[Mark Abraham]

On 22/11/2011 10:41 PM, Javier Romero Garcia wrote:
> Hi, I'm sorry to insist in my question but if somebody could answer or 
> just to send me some information or place to look for, I will be very 
> thanked.

I imagine that these kinds of definitions are discussed in general texts 
on (computational or experimental) modelling of proteins, so that may be 
a good place to start with understanding what g_helixorient might be 
calculating.

>
> GROMACS manual does not give any information but the way to use it. 
> Nothing about the contain of files.

g_helixorient -h has some very basic information that could help. 
Otherwise, I'm sure the GROMACS team regret that the documentation is a 
bit lacking. Please do remember that GROMACS is a volunteer effort. 
Because our resources are finite, it won't always be able to be what we 
would all like it to be. The existence of the g_helixorient tool is 
already rather more than you paid for, too ;-). Do consider using other 
simulation packages' analysis tool sets - often trajectories can be 
inter-converted with little fuss. In extremis, please consider reading 
the code of src/tools/gmx_helixorient.c - but you'll need to be unafraid 
of the mathematics of 3D rotation!

Mark

>
> Thanks again.
>
> ----- Mensaje reenviado -----
> *De:* Javier Romero Garcia <kurcolove at yahoo.com>
> *Para:* "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> *Enviado:* lunes 21 de noviembre de 2011 10:44
> *Asunto:* g_helixorient question
>
> Hello! My name's Javier Romero and I am a PhD student, writting from 
> Barcelona. I am simulating an anphipatic helix of 23 residues, in the 
> interface of a DPPC membrane and water. I am trying to measure the 
> rotation of the helix using the tool "g_helixorient".
>
> Could be somebody so kind to explain me the meaning of each kind of 
> the files? I mean:
>
> - Twist.
> - Tilt.
> - Tetha.
> - Rotation.
> - Rise.
> - Radius.
> - Helixaxis.
> - Center.
> - Bending.
>
> Thanks in advance.
>
>
>
>

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