[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!
>----- 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:
>Thanks in advance.
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