From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Apr 02 2014 - 00:02:58 CDT
Didn't I answer you already?
Well the only way that comes to my mind is modifying velocity restart files,
easy to do if you use "binaryrestart no" in namd config, open the
restart.vel file as pdb with VMD and do something like:
set my400 [atomselect top "resid 1 to 10"]
set my400 {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
Quite easy ;)
Additionally, theres no way I guess to maintain this during simulation.
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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