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

[Ángel Piñeiro]

Dear SA
To be honest I am not sure this can be done by using g_angle, I used my
own code for this calculation. I could send it to you if you send me a
message off the list... but I would prefer to talk with a non-anonymous.

Cheers,

Ángel.




On Wed, 2011-03-16 at 15:58 +0100, 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 ?
> 
> 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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