Re: SMD and CPT?

From: Marcos Sotomayor (
Date: Fri Feb 09 2007 - 12:13:05 CST

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.


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
>> +1 (206) 685 4435
>> +1 (206) 714 4303
>> Postdoc at the Department of Bioengineering
>> at the University of Washington, Seattle WA U.S.A.
>> -----------------------------------------------------

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