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

[sa]

Ok Justin,

So which gmx tool i can use to obtain the angle between two vectors defined
by two atom pairs ?

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.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.
> >      >
> >      >
> >
> >
>
> --
> ========================================
>
> 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
>
> ========================================
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110316/52ee1220/attachment.html>