Re: restarting the simulation

From: JC Gumbart (
Date: Sun Oct 08 2006 - 19:16:13 CDT

You most likely commented out this line:

set temperature 310

which actually just sets a variable named "temperature". You should
always leave that, since you may be using it, as in this case, in
your constant temperature parameters and possibly constant pressure
ones as well. Instead, comment out this line:

temperature $temperature

which actually tells NAMD to initialize to that temperature.

The NAMD Tutorial explains the commands in your configuration file in
detail. You can find it here for your particular platform: http://

On Oct 8, 2006, at 4:17 PM, Dhiraj Srivastava wrote:

> Hi all
> I want to restart my simulation from the minimized and
> equilibrated structure. for that i need to comment out the
> Temperature values from my configuration file. i am using langevin
> dynamics to control the temperature of the system as follows.
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
> but since i am not setting temperature value, this script will
> give me error. if i will not set langevintemp then also i will get
> error message. so what value should i put for langevintemp. should
> i put 310, the temperature at which i have equilibrated my system
> and want to run the simulation?
> --
> Dhiraj Kumar Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211

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