[gmx-users] diverging temperature with pressure coupling

Dommert Florian dommert at icp.uni-stuttgart.de
Mon Apr 18 11:22:26 CEST 2011


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 )

This are just approximate values, exact numbers can be calculated by
g_pme_error for your system.



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
> -- 
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309 
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 198 bytes
Desc: This is a digitally signed message part
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110418/97aa152e/attachment.sig>

More information about the gromacs.org_gmx-users mailing list