[gmx-users] problem with g_energy tool
David van der Spoel
spoel at xray.bmc.uu.se
Mon Jan 1 11:39:57 CET 2007
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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