Re: [gmx-users] g_rms and g_rmsdist on initial structure

Hi, Since gromos-forcefields are not strictly all-atom forcefields, there might be a mismatch between atoms in the two structures. Best, Erik 24 aug 2012 kl. 15.35 skrev Hsin-Lin Chiang: > Hi, > > For example, I have a A.pdb as a initial structure file. > And I just used pdb2gmx on it to gen

[gmx-users] g_rms and g_rmsdist on initial structure

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