Re: Assigning different temperatures to simulation

From: Jhonatam Cordeiro Rodrigues (jcrodrig_at_aggies.ncat.edu)
Date: Thu Apr 03 2014 - 15:24:09 CDT

Thanks Jrme

If I scale up the molecules velocities, the langevin Dynamics would act to
compensate the variation in kinetic energy, eventually scaling back the
temperature of the substrate. Thus it wouldn't be possible to maintain a
constant temperature in the substrate, moreover the transference of kinetic
energy to the drop from the substrate wouldn't be realistic, as the
langevin dynamics would also act to compensate such variation in kinetic
energy.

Is that righ? I know is a quite general answer.

Jhonatam

On Wed, Apr 2, 2014 at 4:16 AM, Jrme Hnin <jerome.henin_at_ibpc.fr> wrote:

> Sorry, I read too quickly. It's scaling by sqrt(400/300), and it's wrong
> for just one reason, a much less obvious one.
>
> I stand half-corrected.
>
> Jerome
>
> ----- Mail original -----
> > Hi Jhonatam,
> >
> > You want to:
> > 1- thermalize everything at 300K
> > 2- run a simulation with a thermostat at 400K acting only on the
> substrate.
> > Do this by supplying a "langevinFile" with coefficients of zero for the
> > liquid.
> >
> > Side remark, scaling velocities by 400/300 is wrong for two reasons.
> What are
> > the two errors? Exercise to the reader. I'll be grading the answers.
> >
> > Cheers,
> > Jerome
> >
> >
> >
> > ----- Mail original -----
> > > Hi Norman
> > >
> > > Thank you for the answer, twice :). I decided to post it on the right
> > > mailing list, as you suggested.
> > >
> > > Cordeiro
> > >
> > >
> > >
> > > On Wed, Apr 2, 2014 at 1:06 AM, Norman Geist
> > > <norman.geist_at_uni-greifswald.de
> > > > wrote:
> > >
> > > > Little error in last post, this should work:
> > > >
> > > >
> > > >
> > > > set my400 [atomselect top "resid 1 to 10"]
> > > >
> > > > $my400 set {x y z} [vecscale [$my400 get {x y z}] [expr
> sqrt(400/300)]]
> > > >
> > > > $my400 delete
> > > >
> > > > set all [atomselect top all]
> > > >
> > > > $all writepdb "mymodifiedrestart.vel"
> > > >
> > > > $all delete
> > > >
> > > >
> > > >
> > > > Norman Geist.
> > > >
> > > >
> > > >
> > > > *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu]
> *Im
> > > > Auftrag von *Jhonatam Cordeiro Rodrigues
> > > > *Gesendet:* Dienstag, 1. April 2014 22:30
> > > > *An:* namd-l_at_ks.uiuc.edu
> > > > *Betreff:* namd-l: Assigning different temperatures to simulation
> > > >
> > > >
> > > >
> > > > Hello
> > > >
> > > >
> > > >
> > > > How would be the proper way for me to assign different temperatures
> for
> > > > different parts of my simulation. I'm trying to assign a temperature
> to a
> > > > substrate (400K) while a liquid on top of it is initially at (300K),
> so
> > > > that I can visualize how the liquid behave during the heat up.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > All the best
> > > >
> > > > Jhonatam Cordeiro
> > > >
> > > > Ph.D student
> > > >
> > > > NCA&T-Department of Industrial Engineering
> > > >
> > > >
> > > > ------------------------------
> > > > <http://www.avast.com/>
> > > >
> > > > Diese E-Mail ist frei von Viren und Malware, denn der avast!
> > > > Antivirus<http://www.avast.com/>Schutz ist aktiv.
> > > >
> > > >
> > >
>

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