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. Thanks, Yolanda _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
