From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Sep 15 2009 - 10:15:23 CDT
On Tue, Sep 15, 2009 at 10:26 AM, Luis Agullo (LAB) <lab_at_lagullo.com> wrote:
> I am completely confused about the difference between temperature
> reassignment and temperature rescaling. I have read NAMD guide and some
> questions about that in this e-mail list (e.g.:
> www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/6401.html), but I am
> very confused yet (probably because I am a newby in MD). Can anybody
> clarify me the basic difference between these two concepts? I want to heat
> my protein smoothly from 0 to 310 and I suppose these parameters can help
> me to do that.
with reassignment you assign new (randomized) velocities to
each coordinate, with rescaling you apply a scaling factor.
both have advantages and downsides. if you want to gently
heat up, then rescaling makes hot spots even hotter. that is
usually not desired. in fact, one always should check wether
the temperature of the solute is at the desired value, as usually
the total system temperature can be misleading (since there are
many more degrees of freedom in the solvent than in the solute).
with reassignment you avoid this problem, but you create a new
one: the kinetic energy of each atom is not longer consistent
with its (local) potential energy and thus needs to be redistributed.
rescaling is usually easier and if you combine it with langevin dynamics
using a large damping coefficient you should be able to dissipate the
energy from the "hot spots" fast enough. also, running a bit of
minimization at the beginning of equilibration helps to 'take off the edge'.
keep in mind that each system can be different, so you have
to always try and check. many people use different protocols
to do this. some are too careless, some waste time by being
overly careful. you have to find a compromise that works.
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com Institute for Computational Molecular Science College of Science and Technology Temple University, Philadelphia PA, USA.
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