Re: [AMBER] Ewald grid size question

From: David A Case <>
Date: Sun, 10 May 2020 21:05:03 -0400

On Sun, May 10, 2020, Yuliana Bosken wrote:

>I have numerous short MD runs from previous group member which I need to
>use for energy calculations. For all runs, the nfft1 and nfft2 values are
>smaller than my box size. I am not sure if the trajectories would be still
>accurate for energy calculations or should we discard them.
>My box size is as follows:
>Ewald parameters:
>verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
>vdwmeth = 1, eedmeth = 1, netfrc = 1
>Box X = 82.822 Box Y = 82.668 Box Z = 86.327
>Alpha = 90.000 Beta = 90.000 Gamma = 90.000
>NFFT1 = 80 NFFT2 = 80 NFFT3 = 120
>Cutoff= 12.000 Tol =0.100E-04
>Ewald Coefficient = 0.22664
>Interpolation order = 4

I don't think you should worry much. The usual procedure in Amber is to
set dsum_tol (the tolerance in the direct Ewald sum) and the cutoff, and
let the program figure out how many grid points to use. This usually
leads to grids that have *about* a 1. Ang spacing.

Users can also decide to set nfft1,2,3 by hand. This is typically an
advanced option, related to a need to get speed in highly parallel
situations, to ensure reproducibility across different numbers of MPI
threads, or the like. But your grid spacings are all about 1 Ang, which
should be fine. There is nothing that says a 1 Ang. spacing is any kind
of magical maximum value.

...hope this helps....dac

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Received on Sun May 10 2020 - 18:30:02 PDT
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