submitting a bugzilla entry could be helpful in examining this case.
On 11/17/2007 4:45 AM, Amadeu wrote:
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 3.3.2 in 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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