From: Norman Geist (
Date: Tue Apr 01 2014 - 00:07:02 CDT

If you only want this behavior from the start and not maintained during
simulation, you could simulate normally 1st and then manipulate the restart
*.vel file by rescaling the velocities of the part of the molecular system
that you want by a factor sqrt(300/400).

You could set “binaryrestart no” and “binaryoutput no” so that the *.vel
files will look like pdb.


PS: This is more a NAMD question ;)


Norman Geist.


Von: [] Im Auftrag von
Jhonatam Cordeiro Rodrigues
Gesendet: Montag, 31. März 2014 15:25
Betreff: vmd-l: Assigning different temperatures in the same simulaiton




Is it possible 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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