[gmx-users] Simulated annealing

Xavier Periole periole at inka.mssm.edu
Wed Jul 30 22:20:01 CEST 2003

1) You can force "genbox" to insert extramolecules of solvent in your box.
    And equilibrate the whole thing, but your peptide conformations have 
    been generated without solvent, right ! HOw good is that ? I am not sure.

2) You can re-do your SAs with explicit solvent ! You beggin with a conformation
    of your peptide. You heat it up to 1000 K run for 50 ps and begin to cool down.
    Much longer, but the size of the system is small. You can compare the 
    structures at the end of the 50ps at 1000K and see if they are different enough.
    If they are you are can assume that you are going to explore enough space.
    ideally. But I'd do more SAs.

Good luck

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