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
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
