Re: [AMBER] DIfferences between thermostats

From: Gustavo Seabra <>
Date: Wed, 23 Nov 2016 18:22:32 -0300


> Em 23 de nov de 2016, à(s) 15:54, Karolina Mitusińska (Markowska) <> escreveu:
> 2016-11-23 17:45 GMT+01:00 Gustavo Seabra <>:
>>> 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”.
> Could you tell something more about how the thermostat could affect MD
> results? And the "net flow”?

Others could give more details here. But, basically, the thermostats give random “pushes” to the molecules, adjusting the velocities so as to conform to a distribution valid at some given temperature.

> By "water flow" I mean something like - watching how water molecules travel
> through the protein and which amino acids are involved into this process.

Is there a directionality involved? Or do you mean just the residence time of the water molecules around some residues? By “flow” I assumed some preferencial direction.

> So could the thermostat change something here?

My point is that the thermostats will affect how the water molecules move, but the effect will be random and in all directions. So, depending on how you measure the flow, in the average you could have some error cancellation and not notice any difference between the different thermostats.

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Received on Wed Nov 23 2016 - 13:30:02 PST
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