[gmx-users] intermolecular energy

[David van der Spoel]

Jones de Andrade wrote:
> Hi all.
> 
> First, I would like to apologize for the previous message. Maybe I've 
> been too "harsh"? Sorry for that.
> 
> Second, I would like to list all the energetic contributions for one 
> (same system, different run) run that g_energy allowed me to get:
> 
> Energy                      Average       RMSD     Fluct.      Drift  
> Tot-Drift
> -------------------------------------------------------------------------------
> Bond                        2.05116  0.0591887          0  - 0.123751   
> -30.9381
> Angle                         2.638  0.0664036          0   0.114896    
> 28.7242
> LJ (SR)                    -14.3726  0.0865671          0 -0.0877988   
> -21.9499
> Disper. corr.             -0.378693 0.00211843          0 -0.00185533  
> -0.463837
> Coulomb (SR)               0.128875  0.0164563          0 0.000956545   
> 0.239138
> Coulomb (LR)             0.00237452 4.3944e-05          0 3.95014e-05 
> 0.00987542
> Coul. recip.               - 145.145   0.660423   0.652976 -0.00137031   
> -0.34258
> Potential                  -10.2211   0.138681          0 -0.0988822   
> -24.7207
> Kinetic En.                 7.67642  0.0990863  0.0988019 0.000103943   
> 0.025986
> Total Energy               -2.54473   0.167497          0 -0.0987789   
> -24.6949
> 
> Temperature                  123.15     1.5896     1.5896 3.34002e-06 
> 0.000835011
> 
> Ok, those are with nmol 500, but it doesn't seem to matter that much. If 
> anybody asks, I can do all them again without that.
had you done this...
> 
> Any help would be really thankfull!
>
If you divide coul. recip by 500 everything is fine. are you using 
twin-range + pme? That seems a strange combination. This is then a 
buglet in g_energy, which does not divide coul recip by nmol. Will fix.
-- 
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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