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.pine...@usc.es <mailto:angel.pine...@usc.es>>
Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue 106
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <1300266404.6843.29.camel@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,
à 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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
