[gmx-users] Time for equilibration

sonali dhindwal sonali11dhindwal at yahoo.co.in
Thu Apr 15 08:40:33 CEST 2010

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.
Sonali Dhindwal

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