AMBER Archive (2008)

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

From: Piyush Wanjari (ppwanjari_at_gmail.com)
Date: Mon Aug 25 2008 - 14:52:37 CDT

Hi David,

Thanks for reply. Yes, I tried running using just one processor and problem
of inhomogeneous system stopped.
for ntt=3, what value of gamma_ln and for ntt=2 what value of vrand should
be used?

Thanks

Piyush

On Fri, Aug 22, 2008 at 10:11 PM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> 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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