[gmx-users] self assembly of protein

[Mark Abraham]

Pednekar Deepa V. wrote:
> Hello all,
> I want to carry out MD simulations to study self assembly of a peptide (34
> residue). Can anyone please let me know the best way of doing it?

There is no simple answer to this question. First, read the literature 
on self assembly of peptides find out if anybody has done it for a 
system anywhere near this large. Then, if the idea still seems 
reasonable, find out how to do MD on normal systems. Then, assemble vast 
amounts of computer time, and hope it works.

Mark