[gmx-users] g_rms and g_rmsdist on initial structure

[Hsin-Lin Chiang]

Hi,

For example, I have a A.pdb as a initial structure file.
And I just used pdb2gmx on it to generate another B.pdb file with 
GROMOS96 43a1 as its force filed.
Then I select C-alpha atoms to calculate RMSD.
echo 3 | g_rms -f B.pdb -s A.pdb
I suppose the RMSD value should be 0, but the value is high to about 0.5nm.
Can someone explain for me?

Sincerely yours,
Hsin-Lin