[gmx-users] Differences in the bonded potentials in 3.3.2 vs. 3.3.1

[Amadeu]

I used the same trp file for both runs, which was created with 3.3.1. I also
tried by creating the trp with the respective grompp version and the same
output resulted. There were no errors or warnings when I ran grompp to
create the trp  file.

        Amadeu

>*
*>* 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
*>*
*>*
*is this with the same tpr file?
If not, please run
gmxcheck -s1 331.tpr -s2 332.tpr

there might be differences in the topology. Does grompp finish without
warnings?
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