[gmx-users] A simple question

[Justin Lemkul]

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 <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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-- 
==================================================

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

==================================================