[gmx-users] A simple question
alexanderwien2k at gmail.com
Wed May 10 22:15:12 CEST 2017
Thanks for response.
But all my energy are contain both kinetic and potential energies.
In "gmx energy ...", I just chose the "Total-Energy" for calculation of the
energies (total energy of the whole system and other U_A, U_B ...), and as
far as I know in the NVT ensemble, the "Total-Energy" is the sum of both
kinetic and potential energies.
I mean in gmx energy ...
..... 8 Disper.-corr.
9 Coulomb-(SR) 10 Coul.-recip. 11 Position-Rest. 12 Potential
13 Kinetic-En. 14 Total-Energy ...
which I invoked separately for each part ... and two by two .., the
= Potential + Kinetic-En as I tested it.
On Wed, May 10, 2017 at 10:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
>> = 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
>> 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
> 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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