[gmx-users] Pressure coupling question

David van der Spoel spoel at xray.bmc.uu.se
Fri Feb 9 22:33:55 CET 2007

toma0052 wrote:
> Hello,
>      I am simulating a lipid bilayer system, and am having some trouble
> understanding the pressure output.  When I run a simulation, even when I do
> not add any perturbations or fix any atoms, the pressure oscillations are
> quite large.  The temperature coupling seems fine.  After about 1ps, the
> system is near the reference temperature, and the oscillations are only about
> 1 or 2 degrees.  So, I expected something, roughly, similar with the
> pressure.  For the pressure, however, my reference pressure is 1.0 bar, but
> the pressure in the system after a few picoseconds seems to range from -400
> to 400 bar.  Is this normal?  Do I just need to wait longer?  Does this mean
> that I did not run the energy minimization long enough and there are some
> high forces?  Is there something else that I am doing wrong?
>      In my mdp file, the pressure coupling looks like:
> Pcoupl           = berendsen
> Pcoupltype       = isotropic
> tau_p            = 0.5
> compressibility  = 4e-5
> ref_p            = 1.0
> I have also tried Parrinello-Rahman pressure coupling with the same result.
> Thanks
> Mike
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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/mailing_lists/users.php
this is normal.
increase your system size to reduce the fluctuations. scales as sqrt(n) :(.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list