On Thu, Jun 16, 2011, Alexander Drozdetski wrote:
> I am trying to run simulations for single ion solvation. I was wondering if
> I need to turn the flag on for NTC=NTF=2 or =1. Since the interactions
> involving hydrogen atoms in the water are important for radial density map,
> turning the interactions off might give me wrong results. Furthermore I was
> wondering if ptraj has a provision for calculating the density of the
> hydration shells. I found ways to find the number of water in the hydration
> shells and also the RDFs in ptraj.
If you are using any of the common TIPx water models, you *must* turn on
SHAKE, since the models were parameterized as rigid waters. Setting ntc to 2
does not "turn interactions off", it just constrains the bonds to their target
values.
...hope this helps...dac
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Received on Fri Jun 17 2011 - 05:00:03 PDT
