On Sun, Nov 25, 2012 at 9:57 PM, Itamar Kass <itamar.kass.monash.edu> wrote:
> Hi,
>
> I am a newbie in amber after few years of using GROMACS. In the GROMOS
> force-field, nonbonded interactions are treated using a twin-range cut-off
> scheme: interactions within the 0.8 nm are calculated every step whereas
> interactions within 1.4 nm are update every 10ps. This is true for both VDW
> and electrostatic interactions, when Reaction-Filed is being used.
Amber does not have a twin-range cutoff scheme to my knowledge, and
multiple time-stepping is atypical in Amber simulations. The default
cutoff for PME simulations is 0.8 nm, where the longer-range electrostatics
are calculated via PME (with the reciprocal space sum being performed every
step).
For implicit solvent calculations, the default cutoff is effectively
infinite. I tend to use 8 Angstroms as my cutoff in PME simulations,
although 9 and 10 angstroms are common as well.
I have search the literature to see what is being used with amber, and
> found variations between 0.8 (cut = 8) to 1.4 nm for the cut-off.
> Assuming I am simulating a proteins/water system using ff12 and PME (for
> the electrostatic calculations), what should be the parameters, and how I
> define them.
I suggest running through the relevant tutorials on
http://ambermd.org/tutorials/ to become acquainted with running simulations
using Amber. The manual has a description of all of the input parameters
and their meanings.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Nov 26 2012 - 06:00:05 PST
