[gmx-users] RMSD

Kay Gottschalk kay.gottschalk at weizmann.ac.il
Sat Jun 21 19:14:01 CEST 2003

Hi there,

I am doing a free md of protein in water with ions, using the GROMOS96 
FF with pressure and T- coupling and PME for electrostatics. I 
positioned the ions with genion -random, as I read in the mailing list 
that the positioning using the best potential is screwed up. Is that 
so? The system equilibrates after 10-15 ps, but with a backbone RMSD of 
~ 0.1 nm to the original structure. Coming from NMR, that seems rather 
high for me. Is this RMSd normal for free MD or do I have a problem? 
What kind of problem might I have (like: start structure not good or 
ions wrongly positioned)? Thanks for your help!

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