[gmx-users] PME
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 7 02:28:27 CEST 2011
Elisabeth wrote:
>
>
> On 6 April 2011 19:28, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Elisabeth wrote:
>
>
>
> On 6 April 2011 15:01, Michael Brunsteiner <mbx0009 at yahoo.com
> <mailto:mbx0009 at yahoo.com> <mailto: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.
>
>
>
> Hi Justin,
>
> I am using PME and extract decomposed Coulmb. SR terms using energy
> groups from g_energy. As we discussed LR terms (coulmb recip) can not be
> decomposed. What I want to make sure about is that at least energy
> groups give reliable PME Coulmb. SR terms.. Reading your statement below
> makes me interpret that both PME related terms i.e SR and LR (coulmb
> recip.) can no be decomposed.
>
Short-range terms can be decomposed pairwise. If you've set the energrygrps
appropriately, you should see that there are various SR terms between each
group. It is the long-range term that is more complicated. Conventional wisdom
is that the PME term cannot be decomposed, but perhaps based on what you've been
presented with earlier, this may not be strictly true. Deriving useful
information may still present a significant challenge.
> so again I am copying your statement : "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."
>
>
> In other words *if one needs to obtain decomposed nonbonded
> intermolecular terms*, PME is not an option and maybe shift potentials
> must be used. Is that what you mean?
>
> I appreciate any clarification on *"PME-related terms"*...
By "PME-related terms," I mean those unique to the PME calculation, i.e. "Coul.
recip." (the mesh term). You've been presented with one possible mechanism to
decompose this term, but as you've been warned, it would require extensive
sampling, high precision, and yet may still be error-prone.
There is a trade-off here. Other (non-PME) electrostatics methods are not as
accurate. Switching and shifting functions are better than plain cutoffs, but
have discontinuities at the switch/shift cutoff, so you get a lot of noise in
the energies. Since you're concerned with calculating intermolecular energies,
then this noise may be extremely problematic.
-Justin
>
> Thanks :)
> Best,
>
>
>
> 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.
>
> -Justin
>
> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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