[gmx-users] stable trajectory?

Ulrich Omasits ulrich.omasits at meduniwien.ac.at
Thu Aug 18 14:05:07 CEST 2005

I'm simulating a protein-ligand system in a 20A-SPC waterbox using the 
gmx-ff and PME.
My problem:
The ligand should be high-affinity but in two out of five 
one-nanosecond-simulations the ligand detaches the protein!
In one simulation the ligand seems to be stable (RMSD & RMSF look nice) 
but then the same simulation performed again (only starting velocities 
differ) delivers totally different results (ligand even detaches!).
How can this happen!?! What can I do?
Should I change the forcefield, the water-type, the box-type, the 
Could these changes affect the trajectory such drastically?


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