Amadeu wrote:
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.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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