My student and I have been trying the latest Gromacs version (3.3.2) for the
simulation of a CNT. We noticed that the bonded energies calculated with
3.3.2 are quite different compared to those from 3.3.1 (see resulting output
below). Has anyone observed similar results? Was anything changed in
3.3.2in how the bonded potentials were calculated? I tried another
case for a
system with harmonic bond and angle potentials, and the bonded energies were
identical for both versions, which makes me believe that the Morse and
G96Angle potentials are somehow different in 3.3.2. Could this be a bug?
--Amadeu
Initial set of energy obtained from the same TPR file. Both output were
obtained with the single precision versions.
*Output from Gromacs-3.3.2:*
Energies (kJ/mol)
Morse G96Angle Proper Dih. LJ (SR) Disper. corr.
5.78994e+03 1.44076e+04 5.47403e+02 -1.57601e+02 -2.46982e+01
Coulomb (SR) Potential Kinetic En. Total Energy Temperature
0.00000e+00 2.05627e+04 3.32197e+01 2.05959e+04 1.11447e+01
Pressure (bar)
-3.06280e+02
*Output from Gromacs-3.3.1:*
Energies (kJ/mol)
Morse G96Angle Proper Dih. LJ (SR) Disper. corr.
4.38162e+01 4.15264e+01 5.53398e+02 -1.57601e+02 -2.46982e+01
Coulomb (SR) Potential Kinetic En. Total Energy Temperature
0.00000e+00 4.56441e+02 9.54848e+00 4.65990e+02 3.20338e+00
Pressure (bar)
-5.04502e+02
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