[gmx-users] g_energy Kinetic Energy

[Justin A. Lemkul]

Hovakim Grabski wrote:
> Dear Gromacs users,
> After running two different simulations, one Hypercin molecule solvated 
> in water and the other one with 2 Hypericin molecules solved in water as 
> well. After that   I used g_energy to extract the kinetic energy of the 
> first simulation,but the values are  pretty high (it's about 5400 kJ/mol 
> and for the second one is 28000 kJ/mol). I wonder if g_energy extracts 
> the energy values from the whole system including the water 
> molecules,and if it is so is there any way to extract the kinetic energy 
> values  of the Hypericin molecules?

g_traj -okt -okr

Note that information derived from velocities does not correct for the presence 
of constraints.  You'll have to do that yourself.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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