[gmx-users] Re: Deshuffling of .xtc file

[Anton Feenstra]

Ivano Eberini wrote:

> I decided to save the full trajectory in the .trr file, but I needed a 
> 'more sampled' file for the protein and I saved it in the .xtc file. I 
> thought I needed to deshuffle also this file (containing just the 
> protein) before proceeding with the analysis.

Shuffling works on molecules - so your protein itself won't get shuffled. 
Even if you have multiple protein molecules, these will remain in the same 
order as they were (but they probably have water inbetween). If you only 
wrote protein to your .xtc file, that should normally correspond exactly to 
  the atom ordering of the protein in your input files.

Having said that, I know from experience that it is very easy to get files 
and file versions (shuffled, de-shuffled, whole system, no water, etc) 
mixed up. Check and double-check everything and give them (very) verbose 
names, like:
topol-shuffled.tpr
confout-shuffled.protein-water.gro
traj-shuffled-protein.xtc
traj-deshuffled-protein.xtc
traj-deshuffled-protein-water.trr


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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