[gmx-users] translation problem in rmsd of dynamic run

[Madhuri Agashe]

Hi,
I have a MD simulation run of 600ps. To analyze the result, I ran the
g_rms command.
What has happened though is that the structure has not changed much, but
has translated along the Z axis after around 300ps. Due to this the
g_rms output does not reflect the correct picture of the structure
remaining unchanged after the dynamics run.
 
Is there an option (or another command) so that the translation can be
ignored and just the structural changes reflected in the RMS output?
 
Madhuri Agashe
Graduate Research Assistant,
Dept. of Bioengineering,
Clemson University,
Clemson, SC 29631
Phone: 864-653-4230 (resi)
            864-656-1352 (off.)
 
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