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

[David van der Spoel]

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