AW: Assigning different temperatures to simulation

From: Norman Geist (
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: [] Im Auftrag
von Jhonatam Cordeiro Rodrigues
Gesendet: Dienstag, 1. April 2014 22:30
Betreff: namd-l: Assigning different temperatures to simulation




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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