[gmx-users] coordinates in xtc vs. trr when using xtc_grps

YOLANDA SMALL yas102 at psu.edu
Wed Jun 21 18:13:52 CEST 2006

Hello All,

I encountered a strange situation that I need some help to clarify.  I ran a
simulation where I exported a subset of atoms from the whole system to an xtc
output file using the xtc_grps option.  I defined the atom numbers for the
xtc_grps in the index file and I also saved the trr output file.  

I am aware that the xtc_grps option reorders the atoms (i.e. atom number 1 in
the xtc output is the first atom listed in the xtc_grps index file which is not
necessarily the first atom in the whole system.)  

With this in mind, I compared the coordinates of the xtc output to the trr
output using the gmxdump command.  The coordinates for the atoms that I thought
I was exporting in the xtc file did not match the coordinates in the trr file. 
Moreover, I found some coordinates in the trr file that were similar to
coordinates in the xtc file but they were for atoms completely unrelated to
those specified in the xtc-grps.

I would expect the coordinates of the specified atoms to be exactly the same in
both the xtc file and the trr file but they are not.  I should mention that I
tested converting the trr file directly xtc using trjconv and I get exactly the
same coordinates in the output.

Is this a bug when usig the xtc_grps option or is there some sort of
transformation being done on the coordinates in the xtc file? 

Any advice is appreciated.


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