[gmx-users] LR electrostatics in single point energy calculations

[rajat desikan]

Hi Justin,
Thanks for the reply. So, must I use a separate .mdp file with infinite
cutoffs for both vdw and coulomb to get all the LR interactions correctly?
Can you give me specific pointers about the settings?



On Wed, Jan 15, 2014 at 11:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/15/14, 11:57 AM, rajat desikan wrote:
>
>> Hi Justin,
>>
>> I meant the pairwise interaction energies and not the total potential
>> energy (I
>> plan to define a 'interaction energy' by summing up all the individual
>> terms). I
>> followed your argument on the total potential energy of the protein being
>> a
>> function of the forcefield.
>>
>> I need the interaction parameters along with the LR terms. I am wondering
>> how to
>> do that.
>>
>> g_energy also gives me only the SR and 14 options. Here is part of a
>> snapshot of
>> the available options:
>>
>> ...
>> 47  Box-Vel-ZZ                              48  Coul-SR:Protein-Protein
>> 49  LJ-SR:Protein-Protein               50  Coul-14:Protein-Protein
>> 51  LJ-14:Protein-Protein                52  Coul-SR:Protein-POPC
>> 53  LJ-SR:Protein-POPC                54  Coul-14:Protein-POPC
>> 55  LJ-14:Protein-POPC                 56  Coul-SR:Protein-SOL
>> ...etc
>>
>>
> There are no "LR" terms unless you use a twin-range cutoff scheme (
> http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy).  The
> PME mesh term is written to the Coul-recip term.  Decomposing it is not
> trivial.
>
> -Justin
>
>
>> On Wed, Jan 15, 2014 at 10:17 PM, Justin Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>>     On 1/15/14, 11:38 AM, rajat desikan wrote:
>>
>>         Hi Justin,
>>
>>         I used the following commands:
>>
>>         mdrun_mpi -s md_6_50ns.tpr -rerun md_6_50ns.gro
>>         gmxdump_mpi -e ener.edr > ener_readme
>>
>>         And in the dump of the ener_readme file, I have the following
>> terms:
>>
>>         Coul-SR:Protein-Protein  -6.62324e+05
>>         LJ-SR:Protein-Protein  -5.64854e+04
>>         Coul-14:Protein-Protein   4.04345e+05
>>         LJ-14:Protein-Protein   3.29438e+04
>>
>>         Coul-SR:Protein-POPC  -1.97403e+03
>>         LJ-SR:Protein-POPC  -4.64531e+03
>>         Coul-14:Protein-POPC   0.00000e+00
>>         LJ-14:Protein-POPC   0.00000e+00
>>
>>         ...etc
>>
>>         There is neither a Coul-recip nor a Coul-LR term. So, I was
>> wondering
>>         about it.
>>         The Coul-recip is the reciprocal space term in a Ewald summation
>>         calculation,
>>         right? I want the total potential energy of the protein. How
>> would I go
>>         about that?
>>
>>
>>     I won't go into why "the total potential energy of the protein" is
>> complete
>>     junk, because I explained all that last week.
>>
>>     I don't know what to expect from gmxdump, but you should probably be
>> using
>>     g_energy instead.
>>
>>
>>     -Justin
>>
>>     --
>>     ==============================__====================
>>
>>
>>     Justin A. Lemkul, Ph.D.
>>     Postdoctoral Fellow
>>
>>     Department of Pharmaceutical Sciences
>>     School of Pharmacy
>>     Health Sciences Facility II, Room 601
>>     University of Maryland, Baltimore
>>     20 Penn St.
>>     Baltimore, MD 21201
>>
>>     jalemkul at outerbanks.umaryland.__edu
>>     <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
>>
>>     ==============================__====================
>>
>>
>>
>>
>>
>> --
>> Rajat Desikan (Ph.D Scholar)
>> Prof. K. Ganapathy Ayappa's Lab (no 13),
>> Dept. of Chemical Engineering,
>> Indian Institute of Science, Bangalore
>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
> --
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore