Re: [AMBER] DIfferences between thermostats

From: Gustavo Seabra <>
Date: Wed, 23 Nov 2016 13:45:47 -0300

> Em 23 de nov de 2016, à(s) 05:14, Karolina Mitusińska (Markowska) <> 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”.

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Received on Wed Nov 23 2016 - 09:00:02 PST
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