2016-11-23 17:45 GMT+01:00 Gustavo Seabra <gustavo.seabra.gmail.com>:
>
> > Em 23 de nov de 2016, à(s) 05:14, Karolina Mitusińska (Markowska) <
> markowska.kar.gmail.com> escreveu:
> >
> > And what about the hydrophobic properties of amino acids? Does the
> > thermostat affect these properties?
>
> It should not. The hydrophobic properties are a function of the force
> field you use.
>
> Now, thinking about it again, you mentioned you are interested in the
> “flow” of water through the protein. In this case, depending on how you
> define “flow”, it is likely that the choice of thermostat will make little
> difference. Yes, the thermostats affect the dynamics of water molecules,
> but it in all directions, which could lead to a fortuitous cancellation of
> errors when you calculate the “net flow”.
>
Could you tell something more about how the thermostat could affect MD
results? And the "net flow"?
By "water flow" I mean something like - watching how water molecules travel
through the protein and which amino acids are involved into this process.
So could the thermostat change something here?
I like this discussion :)
Best regards!
Karolina
>
> Gustavo.
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Received on Wed Nov 23 2016 - 11:00:06 PST
