[gmx-users] isotropic barostat results in anisotropic

Makoto Yoneya yoneya at nanolc.jst.go.jp
Tue Oct 23 09:15:30 CEST 2001

Dear GROMACS stuff:

I'm trying to run GROMACS-3.0.3 with MPI on 32nodes of the IBM RS6K
(recognized as
I'm having trouble to run with isotropic barostat.
My (parallel MPI) job results in anisotropic MD cell scaling only on Y and Z
component sides
nor X side (stay in the initial value).
My setting in grompp.mdp related pressure scaling is as follows.

Pcoupl              =  berendsen
pcoupltype          =  isotropic
tau_p               =  5.0
compressibility     =  4.5e-5
ref_p               =  1.0

I also tried to change the last two lines to be
compressibility     =  4.5e-5 4.5e-5 4.5e-5
ref_p               =  1.0 1.0 1.0
and/or also commented out pcoupltype line, but no changes.

In the corresponding output log, I found

   ePBC                 = xyz
   bUncStart            = FALSE
   etc                  = Berendsen
   epc                  = Berendsen
   epctype              = Isotropic
   tau_p                = 5
   ref_p (3x3):
      ref_p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      ref_p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
      ref_p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
   compress (3x3):
      compress[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      compress[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
      compress[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}.

In these lines, ref_p[0] and compress[0] are all zero and looks strange
compare to the other components.
Any help will be very welcome.

Makoto Yoneya (Dr.)
ERATO Yokoyama Nano-structured Liquid Crystal Project

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