Hi,<div><br></div><div>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:</div>
<div><br></div><div><div> Step Time Lambda</div><div> 900000 900.00000 0.00000</div><div><br></div><div> Energies (kJ/mol)</div><div> U-B Proper Dih. Improper Dih. LJ-14 Coulomb-14</div>
<div> 1.77111e+03 1.22478e+03 1.24096e+02 8.99612e+02 1.07960e+04</div><div> LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) RF excl.</div><div> 2.02487e+04 -7.73436e+02 -1.72259e+05 -1.50772e+03 -5.33117e+03</div>
<div> Potential Kinetic En. Total Energy Temperature Pressure (bar)</div><div> -1.44807e+05 2.84204e+04 -1.16387e+05 3.01479e+02 2.42087e+02</div><div> Constr. rmsd</div><div> 7.88740e-06</div>
<div><br></div><div>Writing checkpoint, step 901680 at Thu Jul 15 08:59:29 2010</div><div><br></div><div>Writing checkpoint, step 931750 at Thu Jul 15 09:14:29 2010</div><div><br></div><div>Writing checkpoint, step 961715 at Thu Jul 15 09:29:29 2010</div>
<div><br></div><div>Writing checkpoint, step 991540 at Thu Jul 15 09:44:29 2010</div><div><br></div><div> Step Time Lambda</div><div> 1000000 1000.00000 0.00000</div><div><br>
</div><div>Writing checkpoint, step 1000000 at Thu Jul 15 09:48:44 2010</div><div><br></div><div> Energies (kJ/mol)</div><div> U-B Proper Dih. Improper Dih. LJ-14 Coulomb-14</div><div> 1.84487e+03 1.18241e+03 1.19723e+02 9.27247e+02 1.08372e+04</div>
<div> LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) RF excl.</div><div> 1.96480e+04 -7.72423e+02 -1.71261e+05 -1.59122e+03 -5.33098e+03</div><div> Potential Kinetic En. Total Energy Temperature Pressure (bar)</div>
<div> -1.44396e+05 2.80310e+04 -1.16365e+05 2.97348e+02 -4.83396e+01</div><div> Constr. rmsd</div><div> 7.88949e-06</div><div><br></div><div> Statistics over 1000001 steps using 200001 frames </div>
<div><br></div><div> Energies (kJ/mol)</div><div> U-B Proper Dih. Improper Dih. LJ-14 Coulomb-14</div><div> 1.78254e+03 1.17488e+03 1.26460e+02 9.19148e+02 1.08095e+04</div><div>
LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) RF excl.</div><div> 1.96458e+04 -7.74885e+02 -1.71741e+05 -1.51523e+03 -5.33115e+03</div><div> Potential Kinetic En. Total Energy Temperature Pressure (bar)</div>
<div> -1.44904e+05 2.84063e+04 -1.16498e+05 3.01329e+02 1.10779e+00</div><div> Constr. rmsd</div><div> 0.00000e+00</div><div><br></div><div> Box-X Box-Y Box-Z</div><div> 5.45508e+00 5.45508e+00 3.85733e+00</div>
<div><br></div><div> Total Virial (kJ/mol)</div><div> 9.47569e+03 2.10309e+00 7.87684e+00</div><div> 1.74263e+00 9.46418e+03 -3.05302e+00</div><div> 8.24251e+00 -2.41221e+00 9.45496e+03</div><div>
<br></div><div> Pressure (bar)</div><div> 2.11556e+00 -2.05272e+00 -2.29518e+00</div><div> -1.94883e+00 2.43768e+00 5.18363e-01</div><div> -2.40126e+00 3.33003e-01 -1.22987e+00</div><div><br></div>
<br></div><div>Moreover, in this particular version of gromacs (git version, 20th June, 2010), RMS fluctuations are not reported in the log file.</div><div><br></div><div>Pooja</div><div><br></div><div><br></div><div><br>
</div><div><br></div><div>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>
</div>