[gmx-users] Ordering with trjorder

[Berk Hess]

> From: ddubov at ngs.ru
> To: gmx-users at gromacs.org
> Date: Fri, 16 May 2008 18:20:02 +0700
> Subject: [gmx-users] Ordering with trjorder
> 
> Dear gmx_users,
> 
> could you clarify me how the "trjorder" procedure works? 
> Manual says "For each frame of the trajectory the selected 
> molecules will be reordered according to..." and so on. 
> Does it mean that the ordering within each frame is 
> INDEPENDENT on the prehistory and further moving of the 
> group? In other words the first (the closest) molecules 
> for different frames may be the different molecules?

Yes.

> 
> For me, I would like to identify some molecules closest to 
> the reference AT THE BEGINNING of my simulation and then 
> to trace their evolution through the whole run. For this 
> purpose the number of each molecule must be no changing 
> from frame to frame! Can I do this with trjorder?

No, but it would not be difficult to modify the tools.
A probable easy solution would be to use trjorder only on the first
frame and write a pdb file as output. You can then look in the pbd file
for the residue numbers of the closest molecules and make an index file.

> 
> And one more striking thing: even when I order each frame, 
> the size of output (ordered) trr-file is about twice less 
> than the size of input trr!

You probably have velocities in your trr, these are not written by trjorder.

Berk.


> 
> With many thanks,
> Dmitri
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