[gmx-users] Re: Computing the total electrostatic energy (short range, 1-4, and Ewald) of an atom

[Mark Abraham]

On 4/04/2012 12:11 AM, Andrew DeYoung wrote:
> Greetings,
>
> Thank you so much, Mark!
>
> Do you know if it is possible to extract just the real-space part (not the
> reciprocal space part) of the Ewald summation?  (By "Ewald summation," I
> mean either the standard Ewald summation or PME.)

That's what Coul-SR is.

Mark

>
> Thank you very much!
>
> Andrew DeYoung
> Carnegie Mellon University
>
>> Hi,
>>
>> Is it possible to compute the total electrostatic energy of an atom over
>> time?  By "total," I mean including all of the terms (short range Coulomb,
>> 1-4 Coulomb, and Ewald), not just the short range Coulomb and 1-4 Coulomb.
>>
>> This question is somewhat related to a question I asked last week (
>> http://lists.gromacs.org/pipermail/gmx-users/2012-March/069745.html ), and
>> to which I received a great answer.  But my specific question now is: is
> it
>> possible to calculate the Ewald term due to a particular atom?  Or is it
>> impossible to decouple the Ewald calculation among individual atoms or or
>> sets of pairs of atoms?
>>
>> For example, I would like to determine the electrostatic energy between
> atom
>> 455 and the "rest" of the system (i.e., all other atoms in the system).
> To
>> try this, I added an entry "a" to my .ndx file:
>>
>> [ a ]
>> 455
>>
>> I then added a directive to my .mdp file:
>>
>> energygrps = a
>>
>> I then run grompp and mdrun, passing my .ndx file to grompp.  (Note: in my
>> .mdp file, I specify that energies should be saved every timestep:
> nstenergy
>> = 1.)  Then I run g_energy on the .edr file that resulted from mdrun.  I
> am
>> given the following energy terms to extract:
>>
>> ---
>>    1  Bond             2  Angle            3  Ryckaert-Bell.   4  LJ-14
>>
>>    5  Coulomb-14       6  LJ-(SR)          7  Coulomb-(SR)     8
>> Coul.-recip.
>>    9  Potential       10  Kinetic-En.     11  Total-Energy    12
>> Conserved-En.
>>   13  Temperature     14  Pressure        15  Constr.-rmsd    16  Vir-XX
>>
>>   17  Vir-XY          18  Vir-XZ          19  Vir-YX          20  Vir-YY
>>
>>   21  Vir-YZ          22  Vir-ZX          23  Vir-ZY          24  Vir-ZZ
>>
>>   25  Pres-XX         26  Pres-XY         27  Pres-XZ         28  Pres-YX
>>
>>   29  Pres-YY         30  Pres-YZ         31  Pres-ZX         32  Pres-ZY
>>
>>   33  Pres-ZZ         34  #Surf*SurfTen   35  Mu-X            36  Mu-Y
>>
>>   37  Mu-Z            38  Coul-SR:a-a     39  LJ-SR:a-a       40
> Coul-14:a-a
>>   41  LJ-14:a-a       42  Coul-SR:a-rest  43  LJ-SR:a-rest    44
>> Coul-14:a-rest
>>   45  LJ-14:a-rest                        46  Coul-SR:rest-rest
>>
>>   47  LJ-SR:rest-rest                     48  Coul-14:rest-rest
>>
>>   49  LJ-14:rest-rest                     50  T-System
>> ---
>>
>> Choices 42 and 44 are two parts of what I would like: short range Coulomb
>> and 1-4 Coulomb energy terms for a-rest.  But is it possible to somehow
> also
>> calculate the Ewald term for a-rest?
>
> Not easily, and the value of it would be debatable even if you could compute
> it. Someone did post a several-step method a few years ago using mdrun
> -rerun and perhaps tpbconv -zeroq that achieved something like the
> decomposition of the reciprocal-space term you seem to be after.
>
> Mark
>