Since you are interested in the water flow through the protein, I would try to measure some flux variable. I’d suggest defining a “boundary surface”, and then counting the number of water molecules that cross this surface in one direction minus the number that cross in the opposite direction, in the same time interval. However, I do not know (from the top of my head) exactly how it would be defined, and it may need some coding to achieve.
—
Gustavo Seabra.
> Em 22 de nov de 2016, à(s) 17:06, Karolina Mitusińska (Markowska) <markowska.kar.gmail.com> escreveu:
>
> Thanks Gustavo and Geoffrey!
>
> I've ran 50ns simulations with different thermostat and in NVE conditions.
> Is there a clever way to compare the water behaviour during these different
> simulations?
> I was thinking about RDF function - could you advise something else?
>
> Thank you for your help!
> Best regards
>
> 2016-11-22 21:05 GMT+01:00 Karolina Mitusińska <mitusinska.gmail.com>:
>
>> Thanks Gustavo and Geoffrey!
>>
>> I've ran 50ns simulations with different thermostat and in NVE conditions.
>> Is there a clever way to compare the water behaviour during these
>> different simulations?
>> I was thinking about RDF function - could you advise something else?
>>
>> Thank you for your help!
>> Best regards
>>
>> 2016-11-22 20:38 GMT+01:00 Geoffrey Gray <gmgray2.mail.usf.edu>:
>>
>>> Depending on the properties you are interested in will determine your
>>> thermostat. Both the Andersen and the Langevin thermostats sample
>>> canonical
>>> distributions, so either will give correct structural configurations and
>>> thermodynamic properties. However, time-dependent properties (such as
>>> diffusion) are not correct, because the thermostats are stochastic and
>>> include random fictitious collisions. If you are interested in transport
>>> properties, such as diffusion coefficients, then a deterministic
>>> thermostat,
>>> such as the Nose-Hoover, is recommended.
>>>
>>> Hope this helps.
>>>
>>>
>>> -----Original Message-----
>>> From: Karolina Mitusińska (Markowska) [mailto:markowska.kar.gmail.com]
>>> Sent: Tuesday, November 22, 2016 2:31 PM
>>> To: AMBER Mailing List <amber.ambermd.org>
>>> Subject: [AMBER] DIfferences between thermostats
>>>
>>> Dear Amber Users,
>>>
>>> I would like to analyse a flow of water molecules through a protein. The
>>> problem is, I'm not sure which thermostat to choose to have the _correct_
>>> behaviour of water molecules. For example if my system have two tunnels
>>> and
>>> one is more hydrophobic than the secnd one - which thermostat should I
>>> choose?
>>>
>>> Sorry for such stupid question. I've spend whole day reading papers about
>>> different thermostats and yet I only know that there could be some
>>> differences in water molecules behaviour, but I still don't understand the
>>> reason of these differences.
>>> Could you help me, please?
>>>
>>> Best regards.
>>> Karolina Mitusińska
>>> PhD student
>>> _______________________________________________
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>>>
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>>>
>>
>>
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Received on Tue Nov 22 2016 - 12:30:03 PST
