AMBER Archive (2007)

Subject: Re: AMBER: protocols for high pressure simulation

From: David A. Case (case_at_scripps.edu)
Date: Tue Aug 28 2007 - 10:41:58 CDT

On Tue, Aug 28, 2007, brmeher_at_iitg.ernet.in wrote:

> I want to perform a simulation of protein under high pressure. So my
> question here is that is there any standard protocol where pressure can be
> raised to a higher level using AMBER force field OR some tricky way to
> perform high pressure simulation ? Also whether the Berendsen coupling is
> appropriate for high pressure simulation or not ? Can any body please help
> me in this regard.

You just set the pres0 variable, and off you go! I don't think this qualifies
as "tricky".

You should certainly check (by a literature search or by experimentation) the
behavior of pure water in whatever water model you plan to use. Few water
potentials have been optimized for high pressure.

I don't know of any reason why the validity of the Berendsen barostat should
depend on the value of pres0, but you might want to check that as well. This
coupling does not rigorously give the NPT ensemble, but the volume fluctuations
it produces at ordinary pressures are pretty accurate nonetheless. (This
comment is just from memory, so you might want to check it out, and repeat at
higher pressures.)

...good luck....dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu