hi, I want to simulate self assembly of several identical proteins, If we use the Insert-molecules command in gromacs and enter the common mdp and cut-off values (for example 1.2 nm) that the force field recommends, Will the proteins that are randomly located at any distance from each other in the simulation box find each other and interact with each other to form assembled structure by molecular Dynamic?? Or should another method or software be used for self assembly of proteins??
any advice or guidance would be greatly appreciated.
Dear Farhad,
sorry to see that your interesting technical question has never received any expert answers. Personally I would not call myself a proven expert in the field of research as we are synthetic inorganic chemists. Just in case that this question is still of interest to you, it migth be worth having a look at the following tutorial:
High throughput peptide self-assembly
http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/tutorial-ht-peptide-gmx5
I hope this link is useful. Good luck with your research and best wishes!
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