Re: Inconsistencies in NAMD simulations

From: Ana Vila Verde (
Date: Tue Jan 22 2008 - 06:14:52 CST

How different are they? Can you quantify them in terms of averages and
standard deviations? If these quantities are similar you have nothing
to worry about.

In general, I would not expect to obtain the exact same results even if
you run with the same parameters. The reason is that the langevin
thermostat is stochastic in nature and thus the trajectory of your
system with differ if you run it twice with the same parameters.

Hope it helps,


Chandra Ramananjara wrote:
> I did an NPT simulation some time ago and I set DCDFreq to 1000. I
> decided this wasn't a high enough sampling rate, so I re-ran the
> simulation (without changing any parameters except setting DCDFreq to
> 500) but I'm getting different energies and pressures. Is this normal
> ? In NAMD, if you run the same simulation twice, is it normal to get
> differing energies ?
> -Chandra
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Ana Vila Verde
Post-doctoral scholar
FOM Institute for Atomic and Molecular Physics [AMOLF]
P.O.Box 41883
1009 DB Amsterdam
The Netherlands
Phone: +31-20-6081392
Fax: +31-20-6684106
University of Minho
Physics Center
Campus de Gualtar
4710-057 BRAGA

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