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

[Yang Ye]

submitting a bugzilla entry could be helpful in examining this case.

On 11/17/2007 4:45 AM, 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
>
>
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>
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