On Wed, Sep 21, 2016, Chitrak Gupta wrote:
>
> I should paraphrase my question to this. What
> is the best way to fix concentration of peptides (multiple molecules) in an
> implicit solvent simulation? Is it possible to define flat-bottom
> positional restraints?
To paraphrase the previous answer:
If the implicit solvent is GB, you cannot do this in Amber. Other codes
(openMM, Tinker) may provide this capability. I don't see that workarounds
like flat-bottom restraints would work.
If the implicit solvent model is RISM, there is a periodic option, so you
could determine a concentration in the usual way (divide the number of
molecules by the volume of the periodic box). But this is both pretty much
untested and so much more expensive that using explicit water that it is hard
to see that anyone would actually use it.
There is some support for periodicity in PB, but my understanding is that this
is not true periodicity, and so would not work for your problem. Ray can
correct me if I'm wrong about this.
...dac
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Received on Thu Sep 22 2016 - 06:30:02 PDT
