Re: Running thermal unfolding with nose hoover langevin piston

From: Neema Salimi (nsalimi_at_msg.ucsf.edu)
Date: Fri Aug 24 2007 - 14:26:55 CDT

I assume you're doing an NPT simulation, since you get a change in
the volume. For doing a simulation like this, it's apparent that
your simulation is not properly equilibrated, unless you're actually
wanting the system to expand. The proper way to do so would be to
equilibrate your water box (either only water or with your protein
fixed) at 510K until the volume is stable, and then begin your
production simulation. And most certainly, you won't want to use a
pressure of 1 bar, as that would be far too low. A pressure of 30
bars would allow liquid water even at 510K. A pressure that's too
high will prevent your protein from unfolding due to too much
compaction.

And the water doesn't "evaporate" because there's no surface from
which it can escape, due to periodic boundary conditions.

On Aug 24, 2007, at 9:53 AM, Zhang, Wei wrote:

> Thanks for your reply.
>
> I have another question. I am running MD simulations at very high
> temperature, e.g. 510K. During the 10ns simulation, the volume of
> the water box is increased 60%, however, at that high temperature,
> shouldn't water evapourate resulting in a much bigger volume?
>
> Anyone knows why?
>
> Thanks again.
>
> Wei Zhang

Neema Salimi
nsalimi_at_msg.ucsf.edu

University of California-San Francisco
Graduate Group in Biophysics
Agard Lab
http://msg.ucsf.edu/agard/
Lab Phone: (415) 476-5143

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