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From: Jason Swails <jason.swails.gmail.com>

Date: Thu, 20 Aug 2015 09:12:14 -0400

On Thu, 2015-08-20 at 09:09 -0300, Hector A. Baldoni wrote:

*> Hi Anu,
*

*>
*

*> Attached you will find some in/out files about how to calculate the
*

*> interaction energies between protein-K+ using anal. You could download
*

*> anal software, compile and learn from the attached file how to use it.
*

*> I hope this will help you.
*

But this does not address Dave's points about the lack of pairwise

decomposability of the GB and PME potential energy functions.

Sure, anal will give you something it *calls* an interaction energy, but

that interaction energy will be a simple, gas-phase (maybe with an

aphysical, distance-dependent dielectric) interaction that bears little

resemblance to the potential energy function you actually run

simulations with these days.

In particular, the interaction between surface atoms of the two species

is treated exactly the same as the interaction between two buried atoms

near the interface. In a solvated environment, this is clearly the

wrong thing to do if what you are interested in is the interaction

energy in solution.

The challenge here is that the GB and PME potentials -- which account

for solvation effects in a more physically sensible model -- are not

pairwise decomposable, so the anal approach will not work here. You

need something different.

For GB, the "pairwise decomposition" coded in sander treats the

effective GB radii as a "constant" derived from the calculated effective

radii of the entire system (when in reality the radii differ between the

"bound" and "unbound" complexes). This approximation makes the GB

potential pairwise decomposable. While approximate, it is almost

certainly better than what anal does.

For PME, the reciprocal sum is definitely not pairwise decomposable, and

pair interaction energies need to be calculated by performing 3 separate

nonbonded energy calculations -- one with the full system, one in which

only the first part of the pair has nonzero nonbonded terms, and one in

which only the second part of the pair has nonzero nonbonded terms. You

still get contributions from the periodic images, so it's still an

approximation, but it's significantly better than what anal did.

I'd not suggest using anal for this purpose. The idecomp=3/4 option in

sander and the 3-calculation PME approach are substantially better, and

may give results that are even qualitatively different from what anal

gives.

HTH,

Jason

Date: Thu, 20 Aug 2015 09:12:14 -0400

On Thu, 2015-08-20 at 09:09 -0300, Hector A. Baldoni wrote:

But this does not address Dave's points about the lack of pairwise

decomposability of the GB and PME potential energy functions.

Sure, anal will give you something it *calls* an interaction energy, but

that interaction energy will be a simple, gas-phase (maybe with an

aphysical, distance-dependent dielectric) interaction that bears little

resemblance to the potential energy function you actually run

simulations with these days.

In particular, the interaction between surface atoms of the two species

is treated exactly the same as the interaction between two buried atoms

near the interface. In a solvated environment, this is clearly the

wrong thing to do if what you are interested in is the interaction

energy in solution.

The challenge here is that the GB and PME potentials -- which account

for solvation effects in a more physically sensible model -- are not

pairwise decomposable, so the anal approach will not work here. You

need something different.

For GB, the "pairwise decomposition" coded in sander treats the

effective GB radii as a "constant" derived from the calculated effective

radii of the entire system (when in reality the radii differ between the

"bound" and "unbound" complexes). This approximation makes the GB

potential pairwise decomposable. While approximate, it is almost

certainly better than what anal does.

For PME, the reciprocal sum is definitely not pairwise decomposable, and

pair interaction energies need to be calculated by performing 3 separate

nonbonded energy calculations -- one with the full system, one in which

only the first part of the pair has nonzero nonbonded terms, and one in

which only the second part of the pair has nonzero nonbonded terms. You

still get contributions from the periodic images, so it's still an

approximation, but it's significantly better than what anal did.

I'd not suggest using anal for this purpose. The idecomp=3/4 option in

sander and the 3-calculation PME approach are substantially better, and

may give results that are even qualitatively different from what anal

gives.

HTH,

Jason

-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Aug 20 2015 - 06:30:03 PDT

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