[gmx-users] problem with g_energy tool
Veera Krasnenko
veera.krasnenko at ut.ee
Sun Dec 31 21:54:41 CET 2006
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
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