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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>>
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Received on Thu Nov 24 2016 - 05:00:02 PST
