On Mon, Dec 16, 2019, Jerome Eberhardt wrote:
>
(Why are you setting up
>periodic condition when I tell you to not do it?!)
The original reason for setting up a "virtual box" when igb=0 and ntb=0
was to re-use the nonbonded list code that was already present for
periodic systems.
This "works" for many systems, but not for ones where atoms can move a
lot from their initial positions. Setting igb=6 was the recommended
workaround for this problem. But the curse of "backwards
compatibility", aka "dusty deck syndrome" means that we (collectively)
never turned off the original option.
>
>### Output imin = 1 ###
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 50 -3.9771E+03 5.8922E+00 1.0709E+02 H1 4340
>
> BOND = 546.2850 ANGLE = 923.4480 DIHED = 2521.1605
> VDWAALS = 2749.6095 EEL = -21571.2602 HBOND = 0.0000
> 1-4 VDW = 872.4954 1-4 EEL = 9640.5688 RESTRAINT = 340.6237
> EAMBER = -4317.6932
>
>### Output imin = 5 ###
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 50 -5.6607E+03 5.5423E+00 7.8322E+01 O 3388
>
> BOND = 541.7428 ANGLE = 769.3931 DIHED = 2506.6400
> VDWAALS = 2494.5050 EEL = -22821.0985 HBOND = 0.0000
> 1-4 VDW = 825.6802 1-4 EEL = 9594.1609 RESTRAINT = 428.2861
> EAMBER = -6088.9764
Do the energies match a step 1?
If you use igb=6, be sure to also use a large cutoff, ideally some value
larger than the size of your system. There is really no other good way
to handle long-range electrostatics for vacuum systems.
....dac
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Received on Mon Dec 16 2019 - 13:00:01 PST
