[gmx-users] Re: Deshuffling of .xtc file
feenstra at few.vu.nl
Mon Nov 29 17:56:37 CET 2004
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
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
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| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
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