Hello All, I have a protein of 576 amino acid long, and has a barell shape topolgy. I have done MD simulation on it for 1ns, and my protein has got distorted shape, i.e, one of the strand became coil and other strands became small. I wrote this query before also, can it be possible that this is due to equilibration conditons i am giving, i am equilibrating it for 100 ps under NVT using brendenson coupling. What should be ideal time for equibrating the protein with solvent ? How should it be determined, or it is based on experimenting with different conditions ? Please help. Regards. -- Sonali Dhindwal
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