Yes, there is directionality involved in these analysis.
2016-11-23 22:22 GMT+01:00 Gustavo Seabra <gustavo.seabra.gmail.com>:
> Hi,
>
> > Em 23 de nov de 2016, à(s) 15:54, Karolina Mitusińska (Markowska) <
> markowska.kar.gmail.com> escreveu:
> >
> > 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”?
>
> 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.
>
> Gustavo.
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Received on Wed Nov 23 2016 - 13:30:04 PST
