From: Eva Gonzalez Noya (evanoya_at_uchicago.edu)
Date: Wed Feb 16 2011 - 10:14:45 CST
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 <evanoya_at_uchicago.edu
> <mailto: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 file).
> Anyone can help with this issue?
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