katesedate at gmail.com
Thu Apr 7 02:10:35 CEST 2011
On 6 April 2011 19:28, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Elisabeth wrote:
>> On 6 April 2011 15:01, Michael Brunsteiner <mbx0009 at yahoo.com <mailto:
>> mbx0009 at yahoo.com>> wrote:
>> 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
>> thinking it through now ... here ER_A0C0, for example, is the
>> 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
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
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"*...
> 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!
>> Elisabeth wrote:
>> > Hello Justin,
>> > Several days ago you answered my question about calculating
>> > 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
>> > 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
>> switch potential) are "Coulomb (SR)."
>> > and also, for a A-B system, I have been using energy groups to
>> > solute-solvent, solvent-solvent, solute-solute terms. Did you
>> mean that
>> > applying doing so with PME as electrostatics treatment is not
>> PME has been consistently shown to be one of the most accurate
>> 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
>> 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.
>> > Thanks for your help!
>> > Best,
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users