AMBER Archive (2008)

Subject: Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!!

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Aug 22 2008 - 22:11:14 CDT

On Wed, Aug 20, 2008, Piyush Wanjari wrote:
>
>
> | Local SIZE OF NONBOND LIST = 41794
> | TOTAL SIZE OF NONBOND LIST = 559211
> ***** Processor 0
> ***** System must be very inhomogeneous.

You can try running the equilibration on just one cpu to see if that
changes things. You might see visually if your system appears to be
inhomogeneous.

> inp2
>
> &cntrl
> imin=0, ntx=1, irest=0, ntpr=100, ntwr=1000, ntwx=100,
> ntwe=500, ntf=2, ntb=1, nstlim=100000,
> temp0 = 300.0, tempi=300.0, ntt=2, tautp=1.0,
                                ^^^^^^^

Setting ntt=2 without setting vrand is probably dangerous. I would
suggest ntt=3 for equilibration. But it's not clear that this is
related to your problem or not.

What happens after the vlimit messages? It could be that you have a
very weird stating configuration, and that a run with real temperature
equilibration would help.

...good luck...dac

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