[gmx-users] xtc files

Yang Ye leafyoung81-group at yahoo.com
Tue Mar 14 05:08:38 CET 2006

> Hi All,
> How do I convert xtc files exported for a subset of atoms in my system to pdb
> files?
> When I run trjconv, I get the following error message:
> Fatal error: Index[0] 3611 is larger than the number of atoms in the trajectory
> file (3152)
> In my mdp file I specify the option 'xtc_grps' to export a subset of solvent and
> protein atoms to an xtc file. This subset of atoms is defined in my index file
> and contains 3152 atoms. Then I discard the .trr files to save space.  It looks
> like the atom index gets renumbered from 1 in the new .xtc file so that the new
> atom indeces no longer correspond to the atoms in the original coordinate file.
Did you use -shuffle -sort? Even in such case, the renumbering won't
take number larger  than the total number of atoms. You may have
selected the group in the index file which includes all the atoms.
More information from you is appreciated.

P.S.: Use gmxcheck -f to check how many atoms inside the xtc.
>  How do I recover the coordinates with matching atom names from the .xtc file?
> Thanks,
> Yolanda
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