From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
Date: Tue Jan 04 2005 - 11:01:53 CST
If you are running periodic boundary conditions I don't think there
should be a boundary energy. If you run non-periodic boundary conditions
then I believe that these additional energy terms are added to the total
300 K is roughly "room temperature", which I believe is the temperature
many in vitro expermiments are carried out at.
Your system will likely not change much in simulations between 300 and
310, unless your protein is cooperative to an extreme. So run at either
Many of the questions you are asking are important to know, and
understand. I suggest you read the documentation on the NAMD site, and do
the online tutorials so you can get a good understanding of how to carry
out MD sims. Also, there are also excellent books by Frenkel, and Leach
that are a good introduction.
On Mon, 3 Jan 2005, Peter Bazeley wrote:
> Hi Ed
> 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
> significant effect.
> 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
> Thanks again,
> Peter Bazeley
> On Mon, 3 Jan 2005 19:29:46 -0500 (EST), Edward Patrick Obrien
> <edobrien_at_glue.umd.edu> wrote:
>> 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:
>>> 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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