AMBER Archive (2005)

Subject: Re: AMBER: Protein dynamics.

From: Yong Duan (duan_at_albert.genomecenter.ucdavis.edu)
Date: Wed Jun 08 2005 - 12:24:02 CDT

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 ...

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