AMBER Archive (2004)

Subject: RE: AMBER: A few questions in the protein unfolding simulations using GB model

From: florent.barbault (florent.barbault_at_paris7.jussieu.fr)
Date: Wed Jan 28 2004 - 06:38:13 CST

Hi,

For me time passed for molecular dynamic simulation is proportional to
degrees of liberty of your system. Therefore is not a simple multiplication
per two. Is your dimer and monomer are solvated? In that case your system is
really much larger for your dimer...
Sincerely yours,
Florent Barbault

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_at_cgl.ucsf.edu>
To: <amber_at_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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