[gmx-users] Pressure coupling

[Sai Pooja]

Hi,

I am aware there have been many threads on this topic and I have looked at
some of them. I would still like to make this query. I am running an npt
equilibration run for a solvated protein using Charmm27-Tip3p (nocmap). I
ran the simulation for 1ns. The average values of pressure converge to 1.1
(ref=1.0), however, the fluctuations are not only large but range from -10^2
--- +10^2. I am pasting an excerpt from my log file here:

           Step           Time         Lambda
         900000      900.00000        0.00000

   Energies (kJ/mol)
            U-B    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    1.77111e+03    1.22478e+03    1.24096e+02    8.99612e+02    1.07960e+04
        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)       RF excl.
    2.02487e+04   -7.73436e+02   -1.72259e+05   -1.50772e+03   -5.33117e+03
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -1.44807e+05    2.84204e+04   -1.16387e+05    3.01479e+02    2.42087e+02
   Constr. rmsd
    7.88740e-06

Writing checkpoint, step 901680 at Thu Jul 15 08:59:29 2010

Writing checkpoint, step 931750 at Thu Jul 15 09:14:29 2010

Writing checkpoint, step 961715 at Thu Jul 15 09:29:29 2010

Writing checkpoint, step 991540 at Thu Jul 15 09:44:29 2010

           Step           Time         Lambda
        1000000     1000.00000        0.00000

Writing checkpoint, step 1000000 at Thu Jul 15 09:48:44 2010

   Energies (kJ/mol)
            U-B    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    1.84487e+03    1.18241e+03    1.19723e+02    9.27247e+02    1.08372e+04
        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)       RF excl.
    1.96480e+04   -7.72423e+02   -1.71261e+05   -1.59122e+03   -5.33098e+03
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -1.44396e+05    2.80310e+04   -1.16365e+05    2.97348e+02   -4.83396e+01
   Constr. rmsd
    7.88949e-06

        Statistics over 1000001 steps using 200001 frames

   Energies (kJ/mol)
            U-B    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    1.78254e+03    1.17488e+03    1.26460e+02    9.19148e+02    1.08095e+04
        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)       RF excl.
    1.96458e+04   -7.74885e+02   -1.71741e+05   -1.51523e+03   -5.33115e+03
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -1.44904e+05    2.84063e+04   -1.16498e+05    3.01329e+02    1.10779e+00
   Constr. rmsd
    0.00000e+00

          Box-X          Box-Y          Box-Z
    5.45508e+00    5.45508e+00    3.85733e+00

   Total Virial (kJ/mol)
    9.47569e+03    2.10309e+00    7.87684e+00
    1.74263e+00    9.46418e+03   -3.05302e+00
    8.24251e+00   -2.41221e+00    9.45496e+03

   Pressure (bar)
    2.11556e+00   -2.05272e+00   -2.29518e+00
   -1.94883e+00    2.43768e+00    5.18363e-01
   -2.40126e+00    3.33003e-01   -1.22987e+00


Moreover, in this particular version of gromacs (git version, 20th June,
2010), RMS fluctuations are not reported in the log file.

Pooja




-- 
Quaerendo Invenietis-Seek and you shall discover.
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