[gmx-users] g_energy Kinetic Energy

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 8 14:10:40 CET 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list