[gmx-users] Rv: g_helixorient question

Javier Romero Garcia kurcolove at yahoo.com
Thu Nov 24 08:36:51 CET 2011

I only just ask for a brief explanation for each file, thanks anyway, the gmx_helixorient.c could be a good solution.

Thanks again for your response.

 De: Mark Abraham <Mark.Abraham at anu.edu.au>
Para: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Enviado: martes 22 de noviembre de 2011 13:00
Asunto: Re: [gmx-users] Rv: g_helixorient question

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!


>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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