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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