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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>
--
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 - 06:00:03 PDT
