Dear David,
I think that there is a discrepancy because from the the different result
((88.04% of Force) and (96.96% of Force).
I thought it was showed that 88.04 % from 100% of non bonded force have
been calculate. But after read your explanation, I understand that I was
wrong.
So if the "non-bonded force" said 228587.86 (88.04% of Force), it is better
than 337191.76 (96.96% of Force) because the first is faster than the
second ? am I correct ?
Thank you for your explanation.
Best Regards,
Setyanto Tri Wahyudi
Lab Biokimia Komputasi ITB-Indonesia
On Mon, Feb 13, 2012 at 7:59 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Feb 13, 2012, setyanto md wrote:
> >
> > There is discrepancy between first and second simulation in the NonBond
> > force calculation.
> > My question is this problem will affect the accuracy of my simulation or
> > not ?
>
> I don't understand why you think there is a discpreancy. If you wish to
> check on accuracy, run short simulations (say 50 steps) with both methods,
> set ntpr=10 (or so) and look at the results, not the timings.
>
> > What is the meaning of "Nonbond force 228587.86 (88.04% of
> Force)" ?
>
> It means the jobs spent 228,000 seconds doing the nonbonded force
> calculation,
> which was 80% of the total time spent calculating forces. Note that the
> numbers you quote are under the "TIMINGS" section of the output.
>
> ....dac
>
>
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Received on Tue Feb 14 2012 - 22:00:02 PST
