[gmx-users] A simple question

Justin Lemkul jalemkul at vt.edu
Wed May 10 22:03:14 CEST 2017

On 5/10/17 3:41 PM, Alex wrote:
> Hello gromacs user,
> Out of a well converged NVT simulation, I calculated the "Total-Energy =
> Utot" as total internal energy of the system which contain three pieces (A,
> B and water).
> Then, using "gmx trjconv" and "gmx mdrun -rerun", "gmx energy", I
> calculated the "Total-Energy" of each piece as U_A, U_B and U_W, using the
> same method, I calculate again the U_AB, U_AB, U_AW ... , which is the
> internal energy due to interaction between two pieces in the soup.
> I expected that summing over U_A, U_B and U_W, U_AB ...., give me the
> "Total-Energy
> = Utot" of the system, but no combination of U_A, U_B and U_W, U_AB ...
> could be equal to the "Total-Energy = Utot" !and the difference is really
> considerable.
> Would you please let me know why so? or I am doing wrong somewhere?

Total energy is the sum of kinetic and potential energy.  No combination of only 
potential energy terms will give the total energy.  They should sum (within 
reasonable numeric precision) to the potential energy of the whole system.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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