[gmx-users] Dimer g_rms
carlajamous at gmail.com
Wed Jun 30 10:34:06 CEST 2010
I'm running my first simulation of a dimer.
When I run g_rms on Calpha (lsq fit and RMSD calculation on Calpha) to get
the RMSD of the whole dimer, the graph is ascending, till reaching a value
of 8 A.
in this case, I take a .tpr file, a .xtc file and a .ndx file of the whole
However, when I run g_rmsd on Calpha, but this time, to get the RMSD of one
chain (one monomer), the graph is constant with value around 1 A. and this
for both chains, when taken alone.
In this case, I take a .tpr file, a .xtc file and a .ndx file of the
So is this an error of using g_rms?
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