Re: AMBER: Protein dynamics.

[Yong Duan <duan|at|albert.genomecenter.ucdavis.edu>]

 If you only need 100+ ps for a small system of 18,000 atoms, I can do it
 on my laptop for you free of charge. This should take no more than a day,
 if that is not too long for you. However, I will use PME instead. PME is
 the method of choice for highly ionic system. Tried others in those early
 "dark days".
 yong
 On Tue, 7 Jun 2005, Laurence Lavelle wrote:
 > Even a small 100 residue protein (approx 1700 atoms) needs approximately
 > 6000 waters (18000 atoms) to appropriately solvate (periodic box, with
 > minimal switched cutoffs so as to avoid protein-protein interactions) the
 > protein in an all atom Amber MD simulation for 100+ ps ...