RE: energy jump between minimization and simulation

From: Bennion, Brian (
Date: Wed Feb 16 2011 - 10:58:33 CST

Are you using binary restart files created from the minimization when you start your dynamics?


From: [] On Behalf Of Eva Gonzalez Noya []
Sent: Wednesday, February 16, 2011 8:14 AM
To: Ajasja Ljubetič
Subject: Re: namd-l: energy jump between minimization and simulation

Thank you very much for your answer.
Actually I tried many things already. I was doing first an NpT (using lagevin pistons) setting the initial velocity close to zero, and also tried NVE but the problem persists

On 2/16/11 3:27 AM, Ajasja Ljubetič wrote:
perhaps the energy jumps due to temperature and/or pressure control?
How are you heating the system?


On Wed, Feb 16, 2011 at 01:06, Eva Gonzalez Noya <<>> wrote:

I found that when running a MD simulation after a minimization the total energy suffers a jump when switching from the minimization to the simulation run (the conf file I am using is copied at the end of this message). In addition there two lines labeled with the same step number (the last step of minimization and the first step of the simulation) and the energy does not much for those neither (I am writing energies every step).
I am not rescaling velocities after the minimization. I am using a constraining harmonic potential on the alpha carbons of the protein both in the minimization and simulation runs (which I perform using a single conf file).
Anyone can help with this issue?

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