From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Feb 16 2011 - 03:27:53 CST
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 <evanoya_at_uchicago.edu>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
> Anyone can help with this issue?
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