[gmx-users] Differences in the bonded potentials in 3.3.2 vs. 3.3.1

David van der Spoel spoel at xray.bmc.uu.se
Fri Nov 16 22:05:23 CET 2007

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 
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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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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