On Mon, May 03, 2010, Rilei Yu wrote:
>
> Recently, I tried to using solvatecap to simulate my system for faster
> speed. Unfortunately, sometime the ligands change drastically, even the
> ligand goes out the binding site in some simulation.
Some setups *are* quite unstable, especially if there are bad contacts in the
initial structure. I don't see anything wrong with your input file per se.
But if you are having troubles, why not try a periodic explicit solvent?
Are you sure that that would be slower to simulate than a non-periodic one
with a 15 Ang cutoff? In any event, trying for "faster speed" is often
a poor objective, especially at the beginning of a study.
...good luck...dac
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Received on Mon May 03 2010 - 07:00:05 PDT
