From: Sterling Paramore (paramore_at_hec.utah.edu)
Date: Fri Feb 09 2007 - 12:53:35 CST
Marcos,
Good points. But I suppose it doesn't matter much either way if the
temperature increase is so negligible. I just wouldn't know how to
interpret my results in a thermodynamic context if the temperature
increase were, say, 20 K, which might be possible in a smaller system.
-Sterling
Marcos Sotomayor wrote:
>
> Actually, I have three reasons to disagree with Sterling.
>
> 1 - Performing simulations in the NVE ensemble permits you to monitor
> the change in energy of your system, and check that it is at least
> similar to the work done by the external applied force (and exactly
> the same when using constant forces). I've monitored temperature
> changes of 0.5 K in simulations that do not use multiple time
> stepping, which matches well the work done on the system by external
> forces.
>
> 2 - Algorithms used to control temperature usually are not designed to
> handle systems in which external forces induce motions in a preferred
> direction. The Langevin thermostat for instance, will apply a net
> (average) zero force to atoms that do not move on a preferred
> direction, but likely will introduce an artificial viscous drag to
> atoms that are being pulled. Thus, your force peaks will be larger.
>
> 3 - Some temperature control methods induced center of mass motion,
> which is not good when you have fixed reference points like in SMD.
>
> The best solution is to perform simulations in both ensembles and
> compare, focusing on those results that are "ensemble independent".
> However, with a water box big enough I suggest to perform SMD
> simulations in the NVE ensemble.
>
> Ginaluca, that's the reason why we performed simulations in the NVE
> ensemble in our Structure paper. Let me know if you have more
> questions, I'll be glad to discuss them with you.
>
> Regards,
> Marcos
>
>
> On Fri, 9 Feb 2007, Sterling Paramore wrote:
>
>> I would definitely suggest you do SMD with a thermostat. Otherwise,
>> the viscous heating that occurs when you pull on your system will
>> increase the temperature. In any real system, the heat produced
>> would be transferred to the surrounding thermal reservoir. The
>> artificial thermostat is just a way to model this effect.
>>
>> -Sterling
>>
>>
>> On Feb 8, 2007, at 11:49 PM, Gianluca Interlandi wrote:
>>
>>> I have a question concerning steered molecular dynamics simulations
>>> (constant force and constant velocity). Is it appropriate to use a
>>> thermostat and barostat (CPT) while performing a constant force or
>>> constant velocity pulling simulation? I have seen that many people
>>> prefer
>>> NVE, i.e., no thermostat.
>>>
>>> I expect my protein to undergo large conformational changes during
>>> pulling. Does a thermostat slow down the sequence of events, since
>>> part of
>>> the applied force is converted into heat?
>>>
>>> Many thanks,
>>>
>>> Gianluca
>>>
>>> -----------------------------------------------------
>>> Dr. Gianluca Interlandi gianluca_at_u.washington.edu
>>> +1 (206) 685 4435
>>> +1 (206) 714 4303
>>> http://biocroma.unizh.ch/gianluca/
>>>
>>> Postdoc at the Department of Bioengineering
>>> at the University of Washington, Seattle WA U.S.A.
>>> -----------------------------------------------------
>>
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