# [gmx-users] A simple question

Alex alexanderwien2k at gmail.com
Wed May 10 22:42:21 CEST 2017

Here are the results, p,s and w are representing a peptide, solid surface
and water, respectively.

Utot = -1340400

us = -1.0173e+06
uw = -382847
up = -805.9
usw = -1.42594e+06
ups = -1.0189e+06
upw = -385347

one combination: (1) \sum uxy = us + uw + up + usw + ups + upw =
-4231139.9  --> \Delta = + 2890739.9

I though that the each of us, uw, up, are being double counted in the (1),

So, I subtracted out them in (2), the result is a bit closer, but still:

(2) : us + uw + up + usw + ups + upw - 2*(us + uw + up) = -1429234.10   -->
\Delta = + 88834.10

Although, there is also a single Na counter-ion in the soup, but the effect
if that can not really compensate the difference: (u_ion = -13.5205 and
u_ionp = -827.121)

In general what should be the right relation between the total internal
energy of a system and internal energies of its constructive segments?

Thanks
Alex

On Wed, May 10, 2017 at 10:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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