[gmx-users] NVE simulations

Sidney Elmer sidnasty at stanford.edu
Tue Jul 9 00:49:05 CEST 2002

I tried starting the NVE simulation from the last snapshot from the
equilibrated NVT ensemble and I still got the same results (ie, the total
energy relaxes to it's minimum value).  I just wanted to emphasize that I'm not
concerned about what the temperature is doing; whether it falls to 0 or goes
through the roof isn't as much of a concern to me as the Total Energy falling
to it's minimum value.  It should be a constant energy simulation (and of
course it will have fluctuations due to the discrete time steps used by the
integrator), but the total energy is not constant.

I should give some context as to why I want a constant Energy simulation.  I am
using a model for Carbon Tetrachloride solvent and I am using a rigid model
using Shake to constrain all distances between carbon-chlorine and
chlorine-chlorine atoms.  Since everything is rigid, I would like to increase
the time step.  Since the root-mean-square-deviation of the total energy in a
microcanonical ensemble is proportional to the time step, I would like to run
several simulations, using different time steps to see just how large I can
make the time step before I run into problems.  It's a simple little exercise.
But since the total energy is not constant when I run without temperature or
pressure control, I'm concerned if there may be a bug or if I'm missing
something in my parameter file that will cause the total energy to remain
constant.  Here is my .mdp file as an attachment.  Thanks for your help on this


PS.  I also received an email for Dr. van der Spoel, that the total energy
should remain constant without temperature or pressure control and no
cut-offs.  I tried running with no cutoffs, but grompp gave me errors that I
could only run without cutoffs if I disables periodic boundary conditions.  I
need pbc, so is there any other way I can run without cutoffs using pdc?  Maybe
cutoffs are the problem that the energy is not constant????  I'd like to check
it out.  Thanks again.

"David L. Bostick" wrote:

> It all depends on that initial configuration and velocities for an NVE
> simulation.  The total energy can remain the same while the temperature
> drops.  This is why in the old days people used to scale their velocities
> each step for some time before actually simulating the system.  You can try
> equilibrating the system in NVT and then change to NVE with initial
> coordinates and velocities taken from the last snapshot of the NVT
> simulation.
> Generally, if the initial configuration is energetically high, the
> temperature will go through the roof.  If it is very low, the potential at
> the starting point will be turned into kinetic energy plus whatever
> velocities you add in the beginning using the velocity generation option
> and the temperature can still fall.
> David
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> David Bostick                                   Office: 262 Venable Hall
> Dept. of Physics and Astronomy                  Phone:  (919)962-0165
> Program in Molecular and Cellular Biophysics
> UNC-Chapel Hill
> CB #3255 Phillips Hall                          dbostick at physics.unc.edu
> Chapel Hill, NC 27599                           http://www.unc.edu/~dbostick
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> On Mon, 8 Jul 2002, Sidney Elmer wrote:
> > Hi,
> >
> > I have a question about the pure MD (constant NVE) application.
> > Whenever I try to run my system at constant Energy, the system always
> > cools down to zero temperature.  Instead of being a constant energy
> > simulation, it appears rather that it is a variant of an energy
> > minimization.  Has anyone else had this happen to them? or is there
> > something that I am missing in my parameter file?  Thanks.
> >
> > Sid
> >
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-------------- next part --------------
title                    = Yo
cpp                      = /lib/cpp
define                   = -DOPLS
integrator               = md 
dt                       = 0.01
nsteps                   = 1000
nstxout                  = 10
nstvout                  = 10
nstlog                   = 50
nstenergy                = 10
nstlist                  = 10
ns_type                  = grid
rlist                    = 2.1
coulombtype              = cut-off
rcoulomb                 = 2.15
rvdw                     = 2.15
gen_vel                  = no
constraints              = none   ;all-bonds
constraint-algorithm	 = shake
pbc                      = xyz

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