[gmx-users] A simple question

[Alex]

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.

Regards,
Alex



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
>> (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
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
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