[gmx-users] g_bundle: angle with x or y axis.

[Justin Lemkul]

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 <jalemkul at vt.edu>
> *To:* Mortuza Munna <mortuza862 at yahoo.com>; Discussion list for GROMACS users
> <gmx-users at 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

========================================