<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:10pt"><div><span>I only just ask for a brief explanation for each file, thanks anyway, the gmx_helixorient.c could be a good solution.</span></div><div><br></div><div>Thanks again for your response.</div><div><br></div> <div style="font-size: 10pt; font-family: arial, helvetica, sans-serif; "> <div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">De:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">Para:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Enviado:</span></b> martes 22 de noviembre de 2011 13:00<br> <b><span style="font-weight: bold;">Asunto:</span></b> Re: [gmx-users] Rv: g_helixorient question<br> </font>
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On 22/11/2011 10:41 PM, Javier Romero Garcia wrote:
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<div><span>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.</span></div>
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<br>
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.<br>
<br>
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</span></div>
<div><span>GROMACS manual does not give any information but the
way to use it. Nothing about the contain of files.</span></div>
</div>
</blockquote>
<br>
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!<br>
<br>
Mark<br>
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<div><span><br>
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<div><span>Thanks again. </span></div>
<div><br>
</div>
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----- Mensaje reenviado -----<br>
<b><span style="font-weight:bold;">De:</span></b> Javier
Romero Garcia <a rel="nofollow" class="yiv1969104472moz-txt-link-rfc2396E" ymailto="mailto:kurcolove@yahoo.com" target="_blank" href="mailto:kurcolove@yahoo.com"><kurcolove@yahoo.com></a><br>
<b><span style="font-weight:bold;">Para:</span></b>
<a rel="nofollow" class="yiv1969104472moz-txt-link-rfc2396E" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">"gmx-users@gromacs.org"</a> <a rel="nofollow" class="yiv1969104472moz-txt-link-rfc2396E" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight:bold;">Enviado:</span></b>
lunes 21 de noviembre de 2011 10:44<br>
<b><span style="font-weight:bold;">Asunto:</span></b>
g_helixorient question<br>
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<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 10pt; font-family: arial, helvetica, sans-serif; ">
<div>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".</div>
<div><br>
</div>
<div>Could be somebody so kind to explain me the
meaning of each kind of the files? I mean:</div>
<div><br>
</div>
<div>- Twist.</div>
<div>- Tilt.</div>
<div>- Tetha.</div>
<div>- Rotation.</div>
<div>- Rise.</div>
<div>- Radius.</div>
<div>- Helixaxis.</div>
<div>- Center.</div>
<div>- Bending.</div>
<div><br>
</div>
<div>Thanks in advance.</div>
</div>
</div>
</div>
<br>
<br>
</div>
</div>
</div>
<br>
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