AMBER Archive (2006)

Subject: Re: AMBER: references

From: simon whitehead (sjw084_at_bham.ac.uk)
Date: Fri Jun 23 2006 - 06:46:22 CDT

Apologies, my question I must have not been clear enough. I am actually
after the correct specirfic reference to cite for using PME in amber 8
and the use of periodic conditions. There are several for PME and was
wondering i should use all

simon

===========================
On Fri, 2006-06-23 at 11:47 +0100, Ricardo J. F. Branco wrote:
> Dear Simon,
>
> You could define periodic boundary conditions using the flag NTB, like in the
> following script:
>
> &cntrl
> ntx=7,iwrap=1,irest=1,
> ntpr=100,ntwx=500,ntwr=-100000,
> nstlim=500000,dt=0.001,
> ntf=2,ntc=2,ntb=2,tol=0.00000001,
> temp0=300.0,ntt=1,tautp=1.0,
> pres0=1.0,ntp=1,taup=1.2,
> &end
>
> Cheers,
>
> RB
>
>
> Quoting simon whitehead <sjw084_at_bham.ac.uk>:
>
> > Dear Amber users,
> >
> > Please could someone tell me the correct reference to use for PME and
> > for the use of periodic boundaries in amber 8?
> >
> > Many thanks
> >
> > simon

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