On 5/10/17 4:14 PM, Alex wrote:
Hi Justin,
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
Total-Energy
= Potential + Kinetic-En as I tested it.
How different are the values? Anything obvious about the value of the
difference? We'll need to see some real numbers here.
-Justin
Regards,
Alex
On Wed, May 10, 2017 at 10:03 PM, Justin Lemkul <jalem...@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
(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
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==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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