Re: SMD and CPT?

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Fri Feb 09 2007 - 12:03:40 CST

Dear Sterling,

Many thanks for you answer. I was wondering why in the paper of Sotomayor,
Corey and Schulten on ankyrin and cadherin repeats they always simulate in
the NVE ensemble (i.e., no thermostat) when they are performing SMD (Table
1 of Sotomayor et al Structure 2005).

Gianluca

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.
> >-----------------------------------------------------
>
>

-----------------------------------------------------
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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