[gmx-users] NVE simulations

Sidney Elmer sidnasty at stanford.edu
Fri Jul 12 21:58:25 CEST 2002

I've never used SPC water, so I may be wrong here, but I can take what I learned from CCL4
and hopefully it will apply to spc water as well.  I would guess that you are really running
with constraints, even when you think you aren't.  In the spc.itp file, the section "settles"
imposes constraints on the water molecules, even if you set the keyword "constraints"
argument to "none" in the .mdp file.  The same thing happened to me with CCL4, where
I defined constraints in the topology file.  You should try using flexspc.itp instead, which
defines bond and angle parameters, and has no constraints built into the topology.  My guess
is that the total energy will remain constant in this case, as long as you set the
"constraints = none" keyword in your .mdp file.  If that doesn't work then I am just as
befuddled about NVE simulations as you.  Good luck.


Nguyen Hoang Phuong wrote:

> > Here is a summary in regards to the problems that I experienced with energy
> > drift in the microcanonical ensemble.  The problem was due to SHAKE.  When
> > I reduced the time step down to 1fs, the total energy of the system
> > *increased*.  So now the behavior of my system in the microcanonical
> > ensemble turned 180 degrees.  I assume from this that it is not a good idea
> > to run SHAKE at all in the microcanonical ensemble, as heat may be
> > transferred unexpectedly.  At least when it is coupled to a heat bath, the
> > problem goes away, since you want heat transfer anyway.  The dummy atom
> > method suggested by Anton is a better approach to increasing the time step
> > in NVE simulations.
> >
> > Finally, when I implemented a flexible model of CCL4 (no constraints at
> > all), there was no energy drift as expected.
> >
> > Sid
> >
> Hi,
> unfortunately, it doesn't help for me. I simulate the peptide in spc water
> and using NVE ensemble. The LJ potential is replaced by Shift and the PME is employed.
> The time step is 0.4fs (0.2fs, 0.6fs,0.8fs,1fs,1.2fs...2fs are tried). Double precision is
> switched on, constrains or without constrains are used (tried for both
> LINCS and SHAKE). However, after 5ps, the total energy is increased about
> 10KJ/mol (Initial energy is -17046KJ/mol. Considering the energy drift is
> too much, I'm wondering how should I do. Anyone have any ideal?
> regards,
> Phuong

More information about the gromacs.org_gmx-users mailing list