From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Apr 02 2014 - 02:35:40 CDT
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
> >
> >
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> >
> >
>
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