AMBER Archive (2009)

Subject: Re: [AMBER] Equilibrium water density

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Jul 15 2009 - 14:53:54 CDT

On Wed, Jul 15, 2009, Myeong Lee wrote:
>
> I tried to equilibrate my system with constant pressure, but found the
> following error after 174 ps. I first heat the system from 0 K to 300 K
> for 20 ps, and tried to equilibrate water density for 500 ps with
> constant pressure.
>
> vlimit exceeded for step 87428; vmax = 40.2588

This can indeed sometimes be hard to track down. Make sure you are using
conservative parameters, dt=0.001, taup > 2.0ps. You may have to run again
until shortly before the crash, save a restart, then go from there with lots
of printout until the problem occurs (if it does).

>
> Also, I'm wondering how long the equilibrium should be done. The
> density was 0.9991 g/cm^3 before it was killed.

Sounds like you are close to the final density.

>
> One more thing, I didn't give restraint for the molecule (dna) while I
> give constant pressure (although I gave restraint during heating) as
> Amber tutorial says. Is this the right way to do?

Yes.

...good luck...dac

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