[gmx-users] g_rms and g_rmsdist on initial structure

Erik Marklund erikm at xray.bmc.uu.se
Fri Aug 24 15:53:25 CEST 2012


Since gromos-forcefields are not strictly all-atom forcefields, there might be a mismatch between atoms in the two structures.



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 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
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Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se

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