Elisabeth wrote:
On 6 April 2011 19:28, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Elisabeth wrote:
On 6 April 2011 15:01, Michael Brunsteiner <mbx0...@yahoo.com
<mailto:mbx0...@yahoo.com> <mailto:mbx0...@yahoo.com
<mailto:mbx0...@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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