Hi all <br><br>This message is related with my previous message (see below) about the calculation of the order value for the DPC alkyl chain in a micelle. So if I understand well the previous angel's message, I need to compute the theta angle between the 2 vectors defined by the (i-1,i+1) and (i, i+2). So for carbon atom C14, I have created an index file with two groups defined as following<br>
<br>aC14 | aC16 and aC14 | aC16 with make_ndx_mpi<br><br>and used the command g_sgangle_mpi -s run_1.tpr -f *.xtc -b 100000 -e 101000 -n index.ndx and choose the C13_C15 and C14_C16 groups. Unfortunately i obtain the following error <br>
<br>Group C13_C15 contains the following atoms:<br>Atomname 0: C13<br>Atomname 1: C15<br>Atomname 2: C13<br>Atomname 3: C15<br>Atomname 4: C13<br>Atomname 5: C15<br>Atomname 6: C13<br>Atomname 7: C15<br>Atomname 8: C13<br>
Atomname 9: C1<br>...<br><br>Group C14_C16 contains the following atoms:<br>Atomname 0: C14<br>Atomname 1: C16<br>Atomname 2: C14<br>Atomname 3: C16<br>Atomname 4: C14<br><br>...<br>Atomname 105: C16<br>Atomname 106: C14<br>
Atomname 107: C16<br><br>Careful: distance only makes sense in some situations.<br><br>Reading frame 0 time 100000.000<br>Back Off! I just backed up sg_angle.xvg to ./#sg_angle.xvg.2#<br><br>-------------------------------------------------------<br>
Program g_sgangle_mpi, VERSION 4.5.3<br>Source code file: gmx_sgangle.c, line: 127<br><br>Fatal error:<br>Something wrong with contents of index file.<br><br>For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>-------------------------------------------------------<br><br>Did I make a error, what is the correct approach. to obtain the angle between 2 vectors ?<br>
<br>Thank you in advance <br><br>SA<br><br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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Message: 3<br>
Date: Wed, 16 Mar 2011 10:06:44 +0100<br>
From: ?ngel Pi?eiro <<a href="mailto:angel.pineiro@usc.es">angel.pineiro@usc.es</a>><br>
Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue 106<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <1300266404.6843.29.camel@arginine><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Then, please, let us know how it works for your systems. The results for<br>
my systems were exactly as expected. This allows to evaluate the order<br>
of the C-chains regardless their orientation... but I do not know if<br>
there is a better method to do this. I would be happy to know the<br>
opinion of anyone else who want to try this or to propose an alternative<br>
method.<br>
<br>
Cheers,<br>
<br>
à ngel.<br>
<br>
<br>
<br>
On Wed, 2011-03-16 at 09:42 +0100, sa wrote:<br>
<br>
> Thank you Angel, I will try your suggestion.<br>
><br>
> Cheers<br>
><br>
> SA<br>
><br>
><br>
><br>
><br>
> Hi<br>
> very recently I faced the same problem with a system that<br>
> gives micelles<br>
> of different geometries and, as far as I saw, g_order don't do<br>
> that.<br>
> Then I decided to compute a kind of local order parameters<br>
> defined as:<br>
><br>
> S_i=(3 cos(\theta)-1)/2<br>
><br>
> where theta is the angle between the segments joining the<br>
> carbon atoms<br>
> (i-1,i+1) and (i, i+2) in a linear C-chain. Perhaps you find<br>
> this<br>
> reasonable for your analysis...<br>
><br>
> Cheers,<br>
><br>
> Ã ngel.<br>
><br>
><br></blockquote></div><br>