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