From: Peter Bazeley (peter.bazeley_at_gmail.com)
Date: Mon Jan 03 2005 - 21:19:33 CST
Thanks for your response. You are right in that there is a gradual
rise in both temperature and kinetic energy, which corresponds to the
rise in total energy. My total simulation time is only 100 ps, so I
imagine that jumping from a temperature of 0 to 300 would have a
I know that in a simple force field equation, potential energy is the
sum of the bond, angle, improper, dihedral, electrostatic, and VDW
energies. Do you know if the boundary and miscellaneous energies get
added to that as well?
It seems that 300K is a very common temperature in NAMD runs, yet
physiological conditions are closer to 310K. Do you know why 300 is
On Mon, 3 Jan 2005 19:29:46 -0500 (EST), Edward Patrick Obrien
> Hi Peter,
> In the microconanical ensemble (NVE) energy drift (change in total
> energy as a function of time) occurs due to finite integration errors
> associated with discretizing newton's equations of motion.
> Typically the total kinetic energy becomes more positive correlating with
> an increase in temperature. You should check these two quantities, and see
> if they are increasing.
> If you are running in the canonical (NVT) or Gibbs (NPT) ensemble your
> total energy should fluctuate.
> You want to avoid energy drift in NVE because it is non-physical, and
> can mess up your dynamics.
> To minimize energy drift make sure your system is well minimized
> (Gradient tolerance < 1.0 or less), heat your sytem in steps (I typically
> due it over the course of 300 ps) to the
> temperature desired, and use a reasonable time integration step
> (conventionally 1 fs at 300K).
> I don't believe you are seeing entropic effect, as the energy you are
> probably looking at is the energy of the system (which neglects the
> entropic term) and not the free energy.
> The minimization step is equivalent to carrying out a simulation at
> temperature equal to 0 K, because the motion is determine only by the
> gradient of the potential energy, and there is no kinetic term. Thus, if
> you did not heat your system up properly, I believe jumping the
> temperature from 0K up to 300 K could lead to bad van der Walls
> interactions, which would cause your energy to drift.
> Hope that helps,
> On Mon, 3 Jan 2005, Peter Bazeley wrote:
> > Hello
> > I am simulating a protein with NAMD, using a basic set of parameters.
> > I minimize my protein for 1000 timesteps, then run for 50000
> > timesteps. I've found that the TOTAL energy of the system increases
> > over time. I guess I'm trying to figure out the reason behind this.
> > Could it be that I am seeing the entropic effects on the protein over
> > time? Or perhaps the minimization created a structure that is lower in
> > energy than would be expected in vivo, and the simulation brings the
> > structure back to a more normal state?
> > Thanks for any input,
> > Peter Bazeley
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