[gmx-users] Re: g_order for DPC alkyl chain in the micelle
Justin A. Lemkul
jalemkul at vt.edu
Wed Mar 16 16:53:09 CET 2011
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.pineiro at usc.es
> <mailto:angel.pineiro at usc.es> <mailto: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>
> > <mailto: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 <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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