sa wrote:
Ok Justin,
So which gmx tool i can use to obtain the angle between two vectors
defined by two atom pairs ?
Well, that's what g_sgangle does. What I said was that if you have to do this
more than a few times (since you have to do every pair of atoms separately),
this can be quite tedious, especially if you have multiple molecules with
multiple angles to calculate.
-Justin
SA
sa wrote:
> Hi all
>
> 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
>
> aC14 | aC16 and aC14 | aC16 with make_ndx_mpi
>
> 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
>
> Group C13_C15 contains the following atoms:
> Atomname 0: C13
> Atomname 1: C15
> Atomname 2: C13
> Atomname 3: C15
> Atomname 4: C13
> Atomname 5: C15
> Atomname 6: C13
> Atomname 7: C15
> Atomname 8: C13
> Atomname 9: C1
> ...
>
> Group C14_C16 contains the following atoms:
> Atomname 0: C14
> Atomname 1: C16
> Atomname 2: C14
> Atomname 3: C16
> Atomname 4: C14
>
> ...
> Atomname 105: C16
> Atomname 106: C14
> Atomname 107: C16
>
> Careful: distance only makes sense in some situations.
>
> Reading frame 0 time 100000.000
> Back Off! I just backed up sg_angle.xvg to ./#sg_angle.xvg.2#
>
> -------------------------------------------------------
> Program g_sgangle_mpi, VERSION 4.5.3
> Source code file: gmx_sgangle.c, line: 127
>
> Fatal error:
> Something wrong with contents of index file.
>
> For more information and tips for troubleshooting, please check
the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Did I make a error, what is the correct approach. to obtain the angle
> between 2 vectors ?
>
Per the description in g_sgangle -h, groups can only be two or three
atoms in
size. It seems as if this tool would be very inefficient for any
more than a
few calculations.
-Justin
> Thank you in advance
>
> SA
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 16 Mar 2011 10:06:44 +0100
> From: ?ngel Pi?eiro <angel.pine...@usc.es
<mailto:angel.pine...@usc.es> <mailto:angel.pine...@usc.es
<mailto:angel.pine...@usc.es>>>
> Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue 106
> To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>>
> Message-ID: <1300266404.6843.29.camel@arginine>
> Content-Type: text/plain; charset="utf-8"
>
> Then, please, let us know how it works for your systems. The
results for
> my systems were exactly as expected. This allows to evaluate
the order
> of the C-chains regardless their orientation... but I do not
know if
> there is a better method to do this. I would be happy to know the
> opinion of anyone else who want to try this or to propose an
alternative
> method.
>
> Cheers,
>
> Ã ngel.
>
>
>
> On Wed, 2011-03-16 at 09:42 +0100, sa wrote:
>
> > Thank you Angel, I will try your suggestion.
> >
> > Cheers
> >
> > SA
> >
> >
> >
> >
> > Hi
> > very recently I faced the same problem with a
system that
> > gives micelles
> > of different geometries and, as far as I saw, g_order
> don't do
> > that.
> > Then I decided to compute a kind of local order
parameters
> > defined as:
> >
> > S_i=(3 cos(\theta)-1)/2
> >
> > where theta is the angle between the segments
joining the
> > carbon atoms
> > (i-1,i+1) and (i, i+2) in a linear C-chain.
Perhaps you find
> > this
> > reasonable for your analysis...
> >
> > Cheers,
> >
> > Ã ngel.
> >
> >
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
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