Thank you!
On Sun, May 10, 2020 at 6:05 PM David A Case <david.case.rutgers.edu> wrote:
> 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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--
Yuliana Bosken
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Received on Sun May 10 2020 - 18:30:02 PDT
