[gmx-users] Deshuffling atoms vs. residues

Jerome Henin jhenin at vitae.cmm.upenn.edu
Tue Aug 1 18:10:10 CEST 2006

On Tuesday 01 August 2006 10:08, David van der Spoel wrote:
> Jerome Henin wrote:
> > Okay, now I have a partial answer to my own question. Apparently, when
> > using the -sort and -shuffle options, the indexfile written by grompp
> > undoes the shuffling, but not the sorting, so to speak. This became clear
> > when I noticed that using just -shuffle without -sort produced the very
> > same indexfile.
> >
> > So let me replace my original question with two and a half questions:
> > 1) Is this the intended behavior, and if so, what's the idea behind it?
> Yes, performance.

I am not sure I am getting this. What impact does is there on performance, 
whether the 'deshuffle' index file restores the original residue order or 
not? Is the problem having to sort residues again for each run in a series?

> > 2) How can I restore the original order?
> Somehow sort your original file and get a desort.ndx from that, but
> there is no gromacs tool for that I'm afraid.

All right, I have written a VMD script that does it. If anyone is interested, 
I will be glad to provide it.


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