On Fri, Apr 02, 2021, Swisher, Justin S wrote:
>
>I'm working on stringing together a polymer. I recently upgraded to Amber16
>and was able to get my polymer solvated in water...
If you have a solute solvated in water, you (presumably) want to run a
periodic simulation. But you are setting ntb=0.
>
>Flags:
>| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
>|Largest sphere to fit in unit cell has radius = NaN
>ASSERTion ' n > 0 ' failed in ew_setup.F90 at line 306.
It's hard to know what sort of simulation you want to run. If you truly
want a non-periodic, vacuum simulation with a very large cutoff, (999.),
then you need to set igb=6. In fact, in most all cases, vacuum simulations
should use igb=6.
But as I said, it's not at all clear that this is what you want. If you
system is "pvcl20_wat", and you have explicit solvent, that sounds like a
periodic simulation. Then the maximum cutoff is roughly half the size of
shortest side of the periodic box.
...hope this helps....dac
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Received on Fri Apr 02 2021 - 18:00:02 PDT
