On 2011-04-18 11.22, Dommert Florian wrote:
Hello,
oh this nasty ILs ;) I am currently investigating a similar problem,
that deals with PR-coupling and my impression is that Leap-Frog is the
problem and not PR. Currently I am running simulations with md-vv and
MTTK to verify my ideas. On the other hand I am using two tc_groups for
my ILs due their difference in size. Unfortunately you have not written
which IL you deal with, but thinking about long chain ILs like
[BMIM][Cl], or [BMIM][PF6], the degrees of freedom for the different
molecules differ strongly. Here the big question is why does the
barostat influence the thermostat. It seems one has to be very very
careful, when choosing the coupling parameter for PR. I did a bunch of
simulations just varying the coupling parameter and obtained large
differences in the dynamics of my system, while static properties like
RDF, density of mass, and pressure look quite fine. For example if I
calculate the conductivity including correlation effects the values
differ from 2 S/m up to 12 S/m. But so far I also have no idea why ???
I am really happy when I finally got my results with vv and if you are
interested I can report back to the list or off-list, just let me know.
On the other hand I do not know if the force field could be a problem.
PR changes the box size according to a Lagrangian equation of motion in
contrast to Berendsen, which just does size rescaling. I do not know how
sensible this equations of motions are in respect to the motion of the
atoms. Perhaps one can try to perform simulation with a higher accuracy
for the electrostatic interactions. I realized that the standard PME
settings are quite poor for ILs. Perhaps the Berendsen pressure coupling
can deal with this, because it forces the box to scale. PR follows its
equations of motions and PERHAPS introduces artefacts if the integration
of atomic trajectories is too inaccurate.
So my PME settings are like this:
rcut=1.3 ( here the force field tells you the number )
pme_order=6
fourierspacing=0.05
rtol=1e-8
This are just approximate values, exact numbers can be calculated by
g_pme_error for your system.
Florian, these PME values are scary! Are you running in double precision
too, otherwise I guess it will be difficult to get the errors as low as
you want them.
As regards the Temperature diversion (no pun intended), this is a known
issue also with Berendsen T,P coupling. The reason for this is lack of
interaction between the different subsystems. It is interesting to hear
the PR makes it worse though, because of the better ensemble properties.
If this also has an effect on dynamic properties all of us are in even
more trouble. I recently had problems reproducing dielectric constants.
I will now redo my simulation with Berendsen P-coupling instead of PR,
even though grompp tells me not to!
Cheers,
Flo
On Sun, 2011-04-17 at 03:10 -0400, Roland Schulz wrote:
Forwarding this email from my group colleague:
Dear Gromacs users,
I am trying to simulate a cellulose fiber in an ionic liquid solution
in the NPT ensemble. During the simulation, the entire system is
coupled to a thermostat. Yet, I observe an inhomogeneous temperature
distribution throughout my system (hot-solvent/cold-solute) when I use
Parrinello-Rahman pressure coupling but NOT when I employ Berendsen
pressure coupling. I have tested velocity-rescaling and the
Nose-Hoover scheme to keep the temperature constant and in both cases
Parrinello-Rahman pressure coupling seems to cause the solute’s
temperature to become significantly lower than the solvent’s (to
decompose temperatures, I am using “mdrun -rerun” with a run input
that defines tc_grps separately).
I was wondering whether there were any known algorithmic reasons for
this unphysical temperature gradient when using Parrinello-Rahman
pressure coupling.
Thank you.
Barmak
Comment from me: The effect is large. The ionic liquid is 5 degrees
higher and the cellulose is 50 degrees lower (after 50ps, after that
it stays constant). With Berendsen pressure both parts fluctuate
around the same target temperature (as one would expect). Any reason
why one doesn't get the correct temperature with rerun? Or is their a
better way to get the temperature for different groups(for a
simulation with just one tc-group)? Any reason why Parrinello-Rahman
pressure coupling would have this effect on the temperature?
Roland
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