Re: SMD and CPT?

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Fri Feb 09 2007 - 12:21:07 CST

On the other hand when I used constant pressure I observed a deformation
of the box along the axis on which the force was applied (using flexible
cell).

 - Cesar
Sterling Paramore escribió:
> 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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