<br>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.
<br><br> Amadeu<br><pre>><i> <br></i>><i> My student and I have been trying the latest Gromacs version (3.3.2) for <br></i>><i> the simulation of a CNT. We noticed that the bonded energies calculated <br></i>
><i> with 3.3.2 are quite different compared to those from 3.3.1 (see <br></i>><i> resulting output below). Has anyone observed similar results? Was <br></i>><i> anything changed in 3.3.2 in how the bonded potentials were calculated?
<br></i>><i> I tried another case for a system with harmonic bond and angle <br></i>><i> potentials, and the bonded energies were identical for both versions, <br></i>><i> which makes me believe that the Morse and G96Angle potentials are
<br></i>><i> somehow different in 3.3.2. Could this be a bug?<br></i>><i> <br></i>><i> --Amadeu<br></i>><i> <br></i>><i> <br></i>><i> Initial set of energy obtained from the same TPR file. Both output were
<br></i>><i> obtained with the single precision versions.<br></i>><i> <br></i>><i> _Output from Gromacs-3.3.2:_<br></i>><i> Energies (kJ/mol)<br></i>><i> Morse G96Angle Proper Dih. LJ (SR) Disper. corr.
<br></i>><i> 5.78994e+03 1.44076e+04 5.47403e+02 -1.57601e+02 -2.46982e+01<br></i>><i> Coulomb (SR) Potential Kinetic En. Total Energy Temperature<br></i>><i> 0.00000e+00 2.05627e+04
3.32197e+01 2.05959e+04 1.11447e+01<br></i>><i> Pressure (bar)<br></i>><i> -3.06280e+02<br></i>><i> <br></i>><i> <br></i>><i> _Output from Gromacs-3.3.1:_<br></i>><i> Energies (kJ/mol)<br>
</i>><i> Morse G96Angle Proper Dih. LJ (SR) Disper. corr.<br></i>><i> 4.38162e+01 4.15264e+01 5.53398e+02 -1.57601e+02 -2.46982e+01<br></i>><i> Coulomb (SR) Potential Kinetic En. Total Energy Temperature
<br></i>><i> 0.00000e+00 4.56441e+02 9.54848e+00 4.65990e+02 3.20338e+00<br></i>><i> Pressure (bar)<br></i>><i> -5.04502e+02<br></i>><i> <br></i>><i> <br></i>is this with the same tpr file?
<br>If not, please run<br>gmxcheck -s1 331.tpr -s2 332.tpr<br><br>there might be differences in the topology. Does grompp finish without <br>warnings?</pre><br>