[gmx-users] Differences in the values of RMSD

Jair jair at iq.ufrj.br
Sat May 14 19:43:16 CEST 2005

I'm trying to calculate the rmsd values using g_rms, but small values are 
produced as compared to VMD values.
I used g_rms in the following way:
g_rms -s prot.tpr -f prot_md.trr -o rmsd.xvg
where the prot.tpr file is the file generated by grompp for the md simulation
I selected Group 4 (Backbone), then
I selected just one group to compare
I selected Group 4 again to do the calculation
RMSD values grows from zero to approximatelly 0.3nm after 5ns of simulation. 
The values of RMSD analyzed with VMD  are between 1.5 nm and of 2.3 nm
They are very different. Where is my mistake?
Thanks for any suggestion

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