On Mon, Jul 01, 2013, James W. Snyder, Jr. wrote:
>
> Also, I am using an explicit solvent model/solvation sphere.
> From what I understood, this warranted using ntb=0 and igb=0.
I'm betting that you would be much better off treating this system with
periodic boundary conditions. It will be *far* faster, and probably more
physically realistic (since you avoid the vacuum/water interface). Even
if you have to add a lot more water molecules to make a big enough box,
you would have a net win.
Although Amber (with enough care) probably can do an NVE simulation as
you are trying to do, it is designed for very different types of simulation.
Basically, the two "designed" options are explicit solvent with ntb=1, or
GB/PB with ntb=0 and igb>0.
...good luck...dac
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Received on Tue Jul 02 2013 - 05:30:03 PDT
