From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Thu Oct 16 2008 - 11:21:55 CDT
Unfortunately, the standard thermostat and barostat of NAMD do not
have a conserved quantity, making it more difficult to monitor the
numerical accuracy of simulations. We are left with either monitoring
the average and fluctuations of energy, temperature and pressure
(which some find sufficient as far as physics goes, while others
strongly disagree), or running NVE simulations, possibly for the sole
purpose of checking their numerical accuracy. Obviously that rules out
any numerical test of the accuracy of the thermostat and barostat.
On Wed, Oct 15, 2008 at 5:23 PM, Audrey Salazar
> As a quick check to ensure that the simulation is running properly, I would
> like to check that the energy of my system, the pressure bath I am using and
> the temperature bath that I am using is conserved. I believe that the TOTAL,
> TOTAL2 and TOTAL3 calculate the total system energy without the pressure and
> temperature bath.
> Is there any way for me to check this?
> Thank you.
> Audrey L. Salazar
> Amaral Research Group
> Dept. of Chemical and Biological Engineering
> Northwestern University
> Evanston, IL USA
> Phone: 847.491.2188
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