Re: total energy stuck between two levels

From: Jim Phillips (
Date: Wed Jan 07 2004 - 09:22:27 CST


I suspect that your outputEnergies period (e.g., 10) is not a multiple of
your fullElectFrequency period (e.g., 4). The logic that avoids the extra
math to calculate ELECT energies that the user never sees doesn't
anticipate this, so half of the energy output are missing the long-range
ELECT energy component. The other energy terms should be OK.

Minimization uses energies directly and therefore always calculates them.


On Tue, 6 Jan 2004, AMIT PALIWAL wrote:

> Hi everyone, I have had this problem with the new namd version 2.5.
> Whenever I simulate peptide in water- first minimize the system and then
> start the production run- in the production run, the total energy
> oscillates beween two levels very far apart. I can not understand why??
> Minimization seems to be perfectly fine. There was a suggestion to use
> separate thermostats for peptide and water. if this is the problem then
> how do you go about doing this? thanks, Amit.

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