Re: SMD and CPT?

From: Sterling Paramore (paramore_at_hec.utah.edu)
Date: Fri Feb 09 2007 - 08:34:21 CST

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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