[gmx-users] mirroring a trajectorie

Justin A. Lemkul jalemkul at vt.edu
Tue May 17 18:56:09 CEST 2011

Thomas Schlesier wrote:
> Hi all,
> is it possible to mirror a trajectorie?
> I have done pulling simulations, where i first pulled two molecules 
> apart and later used the pulled them together (starting form the last 
> frame of the pulling-(apart)-simulation).
> Now want to calculate the rmsd of structures for the path. So i would 
> like to compared first frame of pull-apart with last frame of 
> pull-together ...
> Only way i could think of, would be to write the .xtc into individual 
> .gro-files, then order them and finally put them together to the 
> mirrored .xtc
> This should work, but probably there is an easier way of doing this?

So you're basically looking to play the pull-together trajectory backwards in 
time?  I don't think there's any easier way to do it, but wouldn't it just be 
easier to carry out the normal RMSD analysis and simply renumber the resulting 
times in the .xvg file?  The coordinates are all the same, just in a different 
(but still sequential) order.


> Greetings
> Thomas


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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