[gmx-users] problem with g_energy tool

[David van der Spoel]

Veera Krasnenko wrote:
> Dear All,
> 
> Could you help me to identify what is going wrong in our calculations
> We run g_energy tool with results produced by mdrun (GROMACS).
> And we got the follow output:
> "...
> Statistics over 1500001 steps [ 0.0000 thru 3000.0002 ps ], 5 data sets
> 
> Energy                      Average       RMSD     Fluct.      Drift
> Tot-Drift  -kT ln<e^(E/kT)>
> -------------------------------------------------------------------------------
> Potential                   -586133    1715.72    969.946   -1.63418
> -4902.54         inf
> Kinetic-En.                 46711.9    167.786    167.784 0.000920543
> 2.76163     47433.7
> Total-Energy                -539421    1708.57    958.414   -1.63326
> -4899.78         inf
> Volume                      359.509    1.36219   0.682818 0.00136104
> 4.08312     359.985
> pV                          23.1223     1475.3     1475.3 0.00232535
> 6.97605         inf
> ..."
> As you can see many values are calculated as 'infinite'. This
> happens because energies produced in previous calculation are about 10^5
> kJ. So even e^1000 is pretty big - almost infinite. We tried to
> solve this by modifying equation in sources like this:
> 
> Before: -kT ln<e^(E/kT)>
> After: 1000 * [-kT ln <e^(E/(kT*1000))>]
> 
> Now there is no more 'infinities', but we still have doubts
> - Is it known problem or this is our problems in calculations on previous
> steps or in build ?
> 
> Thank you in advance,
> 
> Vera

What you could try is to subtract the average with the -zero flag. This 
will only work if your fluctuations are small however. In addition you 
should carefully evaluate what the numbers mean. g_energy -h gives you a 
short introduction.

Your result including zero would be:

Ezero - kT ln <e^((E-Ezero)/kT) >

-- 
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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