Occupancy is another useful measure for how frequently water is found in
different parts of the system. You can do this using the volmap tool in VMD.
Best,
Geoffrey
-----Original Message-----
From: Karolina Mitusińska (Markowska) [mailto:markowska.kar.gmail.com]
Sent: Tuesday, November 22, 2016 3:06 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] DIfferences between thermostats
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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Received on Tue Nov 22 2016 - 14:30:02 PST
