Dear Bill,
It is a PC running Linux with two processors. As I repeated the 1 ns
simulation a few times, the average time is about 10-11 days for dimer and
about 2 days for monomer. There was no other job running at the same time. I
assume it is probable due to the way GB model treats the solvent effects on
the molecule's surface but I coulndn't give any theoretical explanations.
Cheers
Jiayun
----- Original Message -----
From: "Bill Ross" <ross.cgl.ucsf.edu>
To: <amber.scripps.edu>
Sent: Tuesday, January 27, 2004 9:19 PM
Subject: Re: AMBER: A few questions in the protein unfolding simulations
using GB model
> > It took 2.5 days to run a 1 ns simulations to the monomeric structure =
> > (164 residues) while it took 12 days to finish a 1 ns run on the dimeric
=
> > structure. This time difference, I think, is a bit surprising.
>
> What platform were you running on? What else was running during
> those times?
>
> Bill Ross
>
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Received on Wed Jan 28 2004 - 12:53:02 PST
