Ok Justin,<br><br>So which gmx tool i can use to obtain the angle between two vectors defined by two atom pairs ?<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;">
sa wrote:<br>
> Hi all<br>
><br>
> This message is related with my previous message (see below) about the<br>
> calculation of the order value for the DPC alkyl chain in a micelle. So<br>
> if I understand well the previous angel's message, I need to compute the<br>
> theta angle between the 2 vectors defined by the (i-1,i+1) and (i, i+2).<br>
> So for carbon atom C14, I have created an index file with two groups<br>
> 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<br>
> 101000 -n index.ndx and choose the C13_C15 and C14_C16 groups.<br>
> 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" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
> -------------------------------------------------------<br>
><br>
> Did I make a error, what is the correct approach. to obtain the angle<br>
> between 2 vectors ?<br>
><br>
<br>
Per the description in g_sgangle -h, groups can only be two or three atoms in<br>
size. It seems as if this tool would be very inefficient for any more than a<br>
few calculations.<br>
<br>
-Justin<br>
<br>
> Thank you in advance<br>
><br>
> SA<br>
><br>
><br>
><br>
> ------------------------------<br>
><br>
> 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> <mailto:<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>
> <mailto:<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>
> Ã 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<br>
> 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>
><br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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