AMBER Archive (2007)

Subject: Re: AMBER: NVT/NPT equilibration issue in GPCR-membrane simulation

From: David A. Case (case_at_scripps.edu)
Date: Fri Jan 26 2007 - 19:45:51 CST

On Fri, Jan 26, 2007, Ross Walker wrote:
>
> In terms of how long to run NPT simulations this is really long enough that
> the density has converged. I.e if the density changes by less than 5% or so
> for a doubling of the run length then you are probably good.
>

I guess I have to object a little here: a 5% change in density is enormous.
In my view, getting the density to be stable to 0.5% (more or less) is a
reasonable goal.

And, just as you can never be too skinny or too rich, it is hard to do too
much equilibration. Complex systems can relax very slowly to equilibrium, and
it can take a *long* time for water (or salt water) to really equilibrate
around even a rigid macromolecule. For a GCPR-membrane simulation you will
probably give up and write up your results long before you have achieved
equilibrium.

...my 2 cents....dac

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