Amadeu wrote:
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.
OK, in that case please submit a bugzilla. Please upload the tpr file,
and include details about your OS, and how gromacs was compiled or
downloaded.
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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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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