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

[Justin A. Lemkul]

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.pineiro at usc.es <mailto: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
>     <mailto: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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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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