[gmx-users] A simple question

[Justin Lemkul]

On 5/10/17 4:41 PM, Alex wrote:
> 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

You're definitely getting double-counting here with the intramolecular nonbonded 
interactions.  Note that both usw and ups are nearly the same as Utot.  The 
total energy of a solid-water and peptide-solid system will have such overlap. 
The total of us + uw + up + (nonbonded energy *only* between usp, ups, upw) 
should roughly sum to Utot.

-Justin

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

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