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.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 23 2016 - 14:30:02 PST
