From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Thu Jun 29 2006 - 16:06:21 CDT
Along many tutorials and papers one could find the some basic protocol
for running a MD simulation, ie.
The second step is recommended to take the system in a gentle way from
0 K to the desired temperature running short simulations in steps of
On NAMD there are several ways to handle temperature control
Which method is best suited for this purpose? It also seems to me that
these methods heat the system in an abrupt way, not in steps. I have
found somewhere on the internet an advice to use a loop to increment the
temperature in steps.
I have also found that the langevin piston is turned on after heating,
during equilibration (for NPT simulations) but not during heating. Can
someone suggest where to find aditional information on these practical
details? Most of the books I have read are focused on the theory of
molecular dynamic simulation methods but not on the practical aspects.
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