On Thu, Oct 15, 2015, Hadeer ELHabashy wrote:
>
> I need to run MD simulation on a small constant volume periodic box
> containing only a crystal of a protein without any solvation.
Aside: are you sure you "need" to do this? The physical realism of the
results is likely to be quite poor: protein crystals always have lots of
waters of solvation.
> I had a problem with the cut off...
How small is your periodic box? Amber requires that the box size be at least
twice the cutoff plus a "skin" of 1 to 2 Ang. The cutoff should not be less
that 8 Ang. (An experienced person might be able to squeeze that down to 7
Ang., but only by knowing what is going on.) This means that the minimum
box size in any dimension is essentially 18 Ang.
If you unit cell is smaller than this, you will need to simulate several unit
cells in order to make the periodic box in Amber big enough. See tutorial
A13 for details on how to do this.
....dac
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Received on Thu Oct 15 2015 - 06:00:03 PDT
