<br>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?<br><br> --Amadeu<br><br><br>Initial set of energy obtained from the same TPR file. Both output were obtained with the single precision versions. <br><br><span style="font-family: courier new,monospace;">
<u>Output from Gromacs-3.3.2:</u><br> Energies (kJ/mol)</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> Morse G96Angle Proper Dih. LJ (SR) Disper. corr.
</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> 5.78994e+03 1.44076e+04 5.47403e+02 -1.57601e+02 -2.46982e+01</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> Coulomb (SR) Potential Kinetic En. Total Energy Temperature</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">
0.00000e+00 2.05627e+04 3.32197e+01 2.05959e+04 1.11447e+01</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> Pressure (bar)</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> -3.06280e+02<br><br><br><u>Output from Gromacs-3.3.1:</u><br> Energies (kJ/mol)<br> Morse G96Angle Proper Dih. LJ (SR) Disper. corr.<br>
4.38162e+01 4.15264e+01 5.53398e+02 -1.57601e+02 -2.46982e+01<br> Coulomb (SR) Potential Kinetic En. Total Energy Temperature<br> 0.00000e+00 4.56441e+02 9.54848e+00 4.65990e+02 3.20338e+00
<br> Pressure (bar)<br> -5.04502e+02<br><br style="font-family: courier new,monospace;"></span><br>