[gmx-users] PME

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 7 01:28:22 CEST 2011

Elisabeth wrote:
> On 6 April 2011 15:01, Michael Brunsteiner <mbx0009 at yahoo.com 
> <mailto:mbx0009 at yahoo.com>> wrote:
>     Elisabeth,
>     You CAN, in fact calculate the contribution of the reciprocal part
>     of the PME energy to the binding energy between two components in
>     a heterogeneous system, its just quite tedious...
>     say, your system is molecules A and B for which you want to know
>     the interaction energy, and the rest of the system, typically
>     the solvent, we call C.
>     Now your total Reciprocal Coulomb energy will have six parts:
>     ER_tot = ER_AA + ER_BB + ER_CC + ER_AB + ER_AC + ER_BC
>     but these parts are NOT given in the gromacs output as they
>     cannot be calculated DIRECTLY, you have to calculate
>     them by setting the charges on A, B, or C (or combinations thereof)
>     to zero (there is a tool for setting the charges in a tpr file
>     to zero) and then do more runs with: "mdrun -rerun" based on the
>     original trajectory to get the required contributions.
>     then E_AB = ER_C0 - ER_A0C0 - ER_B0C0
>     (or something like it, do double check that formula, i can't be bothered
>     thinking it through now ... here ER_A0C0, for example,  is the
>     reciprocal
>     part of the coulomb energy with charges in groups A and C set to
>     zero, etc)
>     this being said ... it's tedious, time-consuming, and error-prone
>     (you need to use double precision and save a lot of frames to
>     get reasonably accurate numbers)
>     You might be better off using reaction field, or PME and simply
>     ignore the reciprocal part altogether (if your molecules A, B
>     are NOT charged and have no permanent and large dipole moment
>     you might get away with the latter)
> Thanks for your elaborate message.
> The point is in my case there is no option other than ignoring LR since 
> LR is not covered by shift or switch functions but at least what PME 
> reports for SR is more accurate. So the decomposed Coulmb. SR terms I am 
> getting using energy groups from PME are "reliable ?

I don't understand your question entirely, so hopefully someone else can comment.

> BTW: I am dealing with non polar particles i.e alkanes and carbon and 
> hydrogen are the only species I have. Can you please tell me about the 
> tool in tpr file that sets all charges to zero..I might use this to 
> check how turning off electrostatics affects properties.

tpbconv -zeroq

> and just a little question: I am unclear about LJ-14 and Coulomb-14 too. 
> Are these included in LJ-SR and Coulomb-SR or for each pair one needs to 
> add up the respective 14 term? i.e A-B LJ-14 + A-B LJ-SR + A-B 
> Coulomb-14 + A-B Coulomb-SR to get nonbonded inter molecular energy for 
> A-B components? If they are already included what is the point of 
> reporting them separately?

1-4 interactions are intramolecular, not intermolecular.  Every nonbonded energy 
term that is listed in the .edr file is a separate entity.


> Thank you so much,
>     What Justin said is correct, PME (or any other Ewald-like
>     method, PPPM, FMA, etc) is standard these days, and for a good reason.
>     However, different properties are affected to a different
>     extent by neglecting the long range interactions, and for
>     what you want to calculate it might be OK for getting at least
>     a qualitative answer, as long as you use PME for the actual MD.
>     (I'd be VERY surprised if everybody who did LIE in the last 10
>     years went through the trouble outlined above)
>     have fun!
>     mic
>     Elisabeth wrote:
>      > Hello Justin,
>      >
>      > Several days ago you answered my question about calculating nonbonded
>      > terms:
>      >
>      > Question: If I want to look at nonboded interactions only, do I
>     have to
>      > add  Coul. recip.  to [ LJ (SR)  + Coulomb (SR) ] ?
>      >
>      > Answer: The PME-related terms contain both solute-solvent,
>      > solvent-solvent, and potentially solute-solute terms (depending
>     on the
>      > size and nature of the solute), so trying to interpret this term
>     in some
>      > pairwise fashion is an exercise in futility.
>      >
>      > my question is if I want to add up nonbonded related terms to get
>     inter
>      > molecular energies, do I have to add Coul. recip. or it is already
>      > included in Coulomb (SR)?
>      >
>     They are separate energy terms.  The PME mesh terms is "Coul.
>     recip." and the
>     short-range interactions (contained within rcoulomb, calculated by a
>     modified
>     switch potential) are "Coulomb (SR)."
>      > and also, for a A-B system, I have been using energy groups to
>     extract
>      > solute-solvent, solvent-solvent, solute-solute terms. Did you
>     mean that
>      > applying doing so with PME as electrostatics treatment is not
>     correct?
>      >
>     PME has been consistently shown to be one of the most accurate
>     long-range
>     electrostatics methods and is widely used, but in your case is
>     preventing you
>     from extracting the quantity you're after (if it can even be
>     reasonably defined
>     at all).  Using energygrps will not resolve the problem I described
>     above.  The
>     "Coul. recip." term contains long-range energies between
>     (potentially) A-B, A-A,
>     and B-B, depending on the nature of what A and B are.  The only
>     terms that are
>     decomposed via energygrps are the short-range terms, which are
>     calculated
>     pairwise.  Thus, with PME, there is no straightforward way to simply
>     define an
>     "intermolecular energy" for a heterogeneous system.  You might be
>     able to define
>     such a term for a completely homogeneous system (which also assumes
>     that the
>     sampling has converged such that the charge densities etc are
>     uniform...but I'm
>     sort of thinking out loud on that), but not one that is a mixture.
>     -Justin
>      > Thanks for your help!
>      > Best,
>      >
>      >
>      >
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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