Hi Gustavo,
so in that case - yes, I expect that water will travel through the protein.
Best regards
Karolina
2016-11-24 13:58 GMT+01:00 Gustavo Seabra <gustavo.seabra.gmail.com>:
> Hi,
>
> What I meant is, do you expect the water to naturally move from one side
> of the protein to the other, like in a water pump? (That’s what I
> understood from “flow”).
>
> —
> Gustavo Seabra.
>
>
>
> > Em 23 de nov de 2016, à(s) 19:45, Karolina Mitusińska (Markowska) <
> markowska.kar.gmail.com> escreveu:
> >
> > Oh, OK, so I misunderstood Gustavo's question.
> > In that case: no, I'm not adding any external force, I want to observe
> > water moving from one place to another (I thought this is related with
> > directionality) and interacting with some amino acids.
> > So, please correct me if I'm wrong, there is no such thing like "the best
> > thermostat" to make water molecules move like "in real life"?
> >
> > Best regards
> > Karolina
> >
> > 2016-11-23 23:43 GMT+01:00 Karolina Mitusińska <mitusinska.gmail.com>:
> >
> >> Oh, OK, so I misunderstood Gustavo's question.
> >> In that case: no, I'm not adding any external force, I want to observe
> >> water moving from one place to another (I thought this is related with
> >> directionality) and interacting with some amino acids.
> >> So, please correct me if I'm wrong, there is no such thing like "the
> best
> >> thermostat" to make water molecules move like "in real life"?
> >>
> >> Best regards
> >> Karolina
> >>
> >> 2016-11-23 23:04 GMT+01:00 David Cerutti <dscerutti.gmail.com>:
> >>
> >>> I think what Gustavo is getting as is a question of whether there is
> some
> >>> external force that is driving the water molecules through some
> channel in
> >>> the protein. If you're just looking at water coming and going as it
> >>> pleases, that's an equilibrium process and Gustavo's guess is a good
> one:
> >>> the thermostats will add randomness that could help your sampling rate,
> >>> but
> >>> with a detailed energy surface like the one present inside a protein
> >>> cavity
> >>> or channel it's anyone's guess as to how a particular thermostat will
> >>> affect the diffusion constant of water. What I can tell you is that if
> >>> you
> >>> run ntt=3 with gamma_ln=3.0 (Langevin thermostat, three frictionless
> >>> collisions per picosecond), you should see the diffusion constant of
> pure
> >>> SPC/E water go from 2.4 cm2/s to about 1.7 cm2/s. The first is
> correct,
> >>> the second is not, but of course the density, heat capacity, and most
> >>> other
> >>> properties of the water remain unaffected. Again, it's veyr hard to
> say
> >>> what a thermostat like that would do to water inside a protein
> channel. I
> >>> couldn't say whether our water models are generally reliable when it
> comes
> >>> to residence times of water on the surface or inside of proteins.
> >>>
> >>> On Wed, Nov 23, 2016 at 4:26 PM, Karolina Mitusińska (Markowska) <
> >>> markowska.kar.gmail.com> wrote:
> >>>
> >>>> 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 Thu Nov 24 2016 - 05:30:02 PST
