On 1/19/13 4:57 PM, Mortuza Munna wrote:
Thank you Justin and Rajat. It is a very helpful information for me indeed. It
seems, I have to write an awk/sed/bash script to rotate each split frame, as I
will have at least 3000 frames after splitting. Moreover, I have 30 simulations
like this. However, is it possible to rotate all the frames together with any
command of Gromacs?
Yes, as I said, it can all be scripted.
1. Run trjconv -sep (names all files like frame1.gro, frame2.gro, etc)
2. For-loop through each file applying editconf -rotate
3. Concatenate
-Justin
Thanks once again.
*/Regards,/*
*/Mortuza
/*
--------------------------------------------------------------------------------
*From:* Justin Lemkul <jalem...@vt.edu>
*To:* Mortuza Munna <mortuza...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
*Sent:* Saturday, January 19, 2013 9:57 AM
*Subject:* Re: [gmx-users] g_bundle: angle with x or y axis.
On 1/18/13 7:09 PM, Mortuza Munna wrote:
> Dear gromacs user,
> I have found that g_bundle can measure the angle between a group from
> index file and z-axis with the option -z. Is it possible to measure the angle
of that group from index file with y-axis/x-axis? Any suggestion will be
appreciable.
>
You cannot do this directly with g_bundle without modifying the source code to
implement such functionality.
One approach would be to:
1. Use trjconv -sep to split your trajectory into individual frames (.pdb or
.gro)
2. Rotate each frame to realign what was previously x or y with the z-axis.
3. Concatenate the frames with trjcat into a new trajectory
4. Apply g_bundle -z
The above approach can easily be scripted.
-Justin
-- ========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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.
Research Scientist
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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