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Hi all,<br>
<br>
After a 3ns MD run, I took a look at the .log file, and found the
potential is positive. How could it be?! I wonder what is the
problem. The standard deviation of density is small, while the SD of
potential is big. Is the system not equilibrated (if yes, why the sd of
density is so small?)? Or there is something wrong with the force
field (I used OPLS-aa, while some parameter of sulfonate are taken from
Ionic liquid publication, because I didn't find related parameters)? Or
something else I have no idea? How to solve it?<br>
<br>
PS: A subsequent md at lower temperature (340K) gives negative
potential, however the sd of potential is still quite big: -819(+-)231
kJ/mol.<br>
<br>
Thanks in advance if you have some suggestions!<br>
<b><br>
<big>Some parameters used:</big></b><br>
gmx 4.0.4, T_couple=Nose-Hoover(400K), P_couple=Parrinello-Rahman
(1bar), PME for coulomb and cut-off for LJ interactions.
rlist=rvdw=rcoulomb=1.0, dt=1fs and constraints=none.<br>
<br>
<b><big>Results in .log file:</big></b><br>
<==== A V E R A G E S ====><br>
<== ############### ======><br>
Energies (kJ/mol)<br>
Bond Angle Proper Dih.
Ryckaert-Bell. LJ-14<br>
7.51939e+03 1.21907e+04 1.12043e+02 9.00085e+03
5.06298e+03<br>
Coulomb-14 LJ (SR) Disper. corr. Coulomb
(SR) Coul. recip.<br>
-4.27726e+03 -9.61433e+03 -7.25985e+02 -3.76464e+03
-1.30800e+04<br>
Potential Kinetic En. Total Energy
Temperature Pressure (bar)<br>
2.42375e+03 2.03489e+04 2.27727e+04 4.00000e+02
1.48081e+00<br>
<br>
Box-X Box-Y Box-Z
Volume Density (SI)<br>
3.45196e+00 3.45196e+00 3.45196e+00 4.11340e+01
1.12914e+03<br>
pV<br>
1.27896e-01<br>
<====== ############################### ==><br>
<==== R M S - F L U C T U A T I O N S ====><br>
Energies (kJ/mol)<br>
Bond Angle Proper Dih.
Ryckaert-Bell. LJ-14<br>
1.63642e+02 1.84279e+02 6.75325e+00 1.01384e+02
5.80187e+01<br>
Coulomb-14 LJ (SR) Disper. corr. Coulomb
(SR) Coul. recip.<br>
2.44975e+01 9.62751e+01 3.70809e+00 6.08742e+01
3.71360e+01<br>
Potential Kinetic En. Total Energy
Temperature Pressure (bar)<br>
2.73923e+02 2.61094e+02 3.90285e+02 5.13234e+00
1.21958e+03<br>
<br>
Box-X Box-Y Box-Z
Volume Density (SI)<br>
5.87539e-03 5.87539e-03 5.87539e-03 2.10006e-01
5.76728e+00<br>
<br>
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