# [CP2K-user] free energy of a trajectory starting from a transition state

jennifer fuyu... at gmail.com
Sun Mar 29 21:55:50 UTC 2020

```Dear Sirs.
I was trying to propagate trajectories using AIMD. I was asked to start
from a very high energy intermediate (similar energy as the transition
state) and see the product distribution.Then I need to get the activation
energy of the product formation from the high energy intermediate. So I
turn to MD as the following input setup. Then I get .ener file. I noticed
that the cons Qty is not constant and shift a lot at the end of the
trajectory. The final products are exactly what we would expect. I was
wondering if such way of running trajectories is scientific meaningful
regarding to predict product distribution* and whether the sum of kin and
pot is the free energy for the system. If not, how I can calculation the
free energy of MD simulation? *Last question is about Cons Qty. The
simulation starts after simple optimization without equilibration (which is
not possible cause our initial geometry is very high in energy and
equilibrium will lead it to pdt directly).But the Cons Qty tells us the
system is not fully equilibriumed so not reasonable.* How should I set up
MD from high energy intermediates/transition states?*
Thanks

*  &MD*
*    ENSEMBLE NVT  *
*    TEMPERATURE [K] 298.15 *
*    TIMESTEP [fs] 0.5*
*    STEPS 50000 *
* &THERMOSTAT*
* &NOSE*
*      LENGTH 3*
*      YOSHIDA 3*
*      TIMECON 100.0*
*      MTS 2*
*    &END NOSE*
* &END THERMOSTAT *

*.ener*

*#     Step Nr.          Time[fs]        Kin.[a.u.]          Temp[K]
Pot.[a.u.]        Cons Qty[a.u.]        UsedTime[s]         0
0.000000         0.256346498       298.150000000     -1045.692256885
-1045.435438294         0.000000000         1            0.500000
0.251739701       292.791953385     -1045.687561911     -1045.435241155
16.035605922         2            1.000000         0.246770279
287.012147241     -1045.682578277     -1045.435120246         2.770686112
3            1.500000         0.243348534       283.032403503
-1045.679265278     -1045.435124527         2.778688506         4
2.000000         0.241726793       281.146199212     -1045.677792961
-1045.435171152         2.780995430         5            2.500000
0.241375809       280.737977961     -1045.677567598     -1045.435195062
2.386485098         6            3.000000         0.241853544
281.293619726     -1045.678163310     -1045.435211988         2.792329600
7            3.500000         0.242774676       282.364964657
-1045.679229318     -1045.435256191         2.387376870         8
4.000000         0.243440523       283.139394116     -1045.680060966
-1045.435321621         2.795848448         9            4.500000
0.242913307       282.526202203     -1045.679685038     -1045.435373115
2.785384228        10            5.000000         0.240445208
279.655620257     -1045.677316071     -1045.435373698         2.388625912
11            5.500000         0.236022714       274.511931925
-1045.672927474     -1045.435311187         2.788325803        12
6.000000         0.230602733       268.208091694     -1045.667489394
-1045.435199588         2.787662090...     29647        14823.500000
0.267209250       310.784186822     -1045.792584736     -1044.698640663
2.457661132     29648        14824.000000         0.263518275
306.491309460     -1045.788962431     -1044.698581242         2.866651712
29649        14824.500000         0.259648762       301.990778207
-1045.785134708     -1044.698495486         2.858745218     29650
14825.000000         0.256924523       298.822286300     -1045.782459885
-1044.698417876         2.454754142     29651        14825.500000
0.256586508       298.429150545     -1045.782209988     -1044.698378761
2.857808102     29652        14826.000000         0.259300911
301.586201573     -1045.785071671     -1044.698397266         2.856152027*
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