Thank you Jason,
I understand better now.
Best regards,
Cat
> Date: Mon, 12 Sep 2011 08:54:51 -0400
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Why cut=999.9 was used in Tutorial A7 for REMD calculation?
>
> On Mon, Sep 12, 2011 at 2:30 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> >
> > Dear AMBER Experts,
> > In Tutorial A7 for REMD calculation (input file is listed below), I noted
> > that cut =999.0 and rgbmax=999.0 was used, but in tutorial 1, cut = 12.0 was
> > used for GB calculations. I found both tutorial A7 and 1 are also done at GB
> > solvent envirnoment. Could you mind teach me why such a large cut value
> > should be used in REMD calculation?
> >
>
> You need to use a large cutoff for GB calculations because electrostatic
> interactions vary as 1/r, which is a very slowly decaying function. In
> fact, the sum of the 1/r sequence diverges for all positive integers r.
> (Indeed, if you integrate the function 1/r from 1 to infinity the integral
> diverges). Therefore, electrostatic interactions are what we call
> long-range, and your cutoff has to be infinite (or larger than your system
> size) for implicit solvent calculations to include all EEL pairs.
>
> For explicit solvent simulations, the cutoff only affects VDW interactions
> (which scale as 1/r^6, so they decay much more quickly) since PME includes a
> reciprocal space sum to handle the long range electrostatic interactions.
>
> One last tip I'd give is to read tutorial B1 carefully. It walks you
> through a demonstration of different simulation protocols. It uses both a
> 12 Å cutoff and a 999 Å cutoff in order to demonstrate the difference
> between the two approaches. It never endorses a 12 Å cutoff over an
> infinite cutoff (in fact it does the opposite, at least for vacuum
> simulations).
>
> HTH,
> Jason
>
> > Many thanks,
> > Catherine.
> > ========================================Equilibration
> > &cntrl
> > irest=0, ntx=1,
> > nstlim=500, dt=0.002,
> > irest=0, ntt=3, gamma_ln=1.0,
> > temp0=XXXXX, ig=RANDOM_NUMBER,
> > ntc=2, ntf=2, nscm=1000,
> > ntb=0, igb=5,
> > cut=999.0, rgbmax=999.0,
> > ntpr=100, ntwx=1000, ntwr=100000,
> > nmropt=1,
> > numexchg=1000,
> > /
> > &wt TYPE='END'
> > /
> > DISANG=ala10_chir.dat=====================================
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Mon Sep 12 2011 - 11:00:02 PDT
