On Sun, Mar 03, 2019, Xiaocong Wang wrote:
>I am trying to calculate the energies of a solvated glucose with TIP5P
>water in truncated octahedron box. I am doing a one step energy
>minimization to evaluate the energy of the system in the trajectory.
>The system has the box dimension of over 60 angstrom. There are no
>periodic boundaries in either topology and trajectory file. The energy
>calculation would die even at the first step.
>
>The error is:
>
>minimizing coord set # 1
>---------------------------------------------------
>
> eedmeth=4: Setting switch to one everywhere
>
>---------------------------------------------------
>Frac coord min, max: 0.45443913178870859 1.0144599523215547
>The system has extended beyond
> the extent of the virtual box.
This is a "virtual" box to make sander able to treat some parts of a
system as periodic even when it is not.
If you get this with a single step minimization, it sounds like
something may be wrong, but it's hard to see what, based on this
information.
Try running with igb=6, which is a better way to carry out non-periodic
simulations (doesn't make use of any "virtual box").
...good luck...dac
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Received on Tue Mar 05 2019 - 07:00:01 PST
