[gmx-users] g_order for DPC alkyl chain in the micelle

[sa]

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 ?

Thank you in advance

SA



> ------------------------------
>
> Message: 3
> Date: Wed, 16 Mar 2011 10:06:44 +0100
> From: ?ngel Pi?eiro <angel.pineiro at usc.es>
> Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue 106
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1300266404.6843.29.camel at 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.
> >
> >
>
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