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From: Wesley Michael Botello-Smith <wmsmith.uci.edu>

Date: Mon, 9 Jul 2018 09:45:13 -0700

In the case of linear solutions to the poisson boltzmann-equation, the

ionic strength term is most easily conceptualized as a perturbation of the

diagonal elements of the matrix representation of the discretization of the

differential equations being solved numerically.

For the non-linear case, the mathematics is indeed a bit too complex to be

easily represented in an email.

As for a previous question on whether or not to include protein

contribution: In PBSA this depends on your choice of boundary conditions

(see manual for appropriate flag to control this). For linear PBSA, you

have 3 choices: Zero potential boundary, Free Boundary, and Periodic

Boundary.

1) The first is probably the least helpful to you, but in essence, zero

potential boundary (also called Dirichlet boundaries in some cases) would

be akin to placing the system inside a small cavity within an infinite

conductor. Conceptually, you could think of it like carving out a nanometer

scale cube (or rectangular prism) inside a non-reactive metal block and

filling it with your system.

In this case, the protein would quite certainly be contributing and would

represent something akin to a single molecule experiment. In some sense,

the boundaries of the system act like electrostatic 'mirrors' so the

protein essentially sees its inverse charge image right at the boundary. So

this case is where the effects of the protein's charge distribution are

most pronounced

2) For Free Boundary conditions, this conceptually represents the infinite

dilution setup that Dr. Case mentioned earlier. In that case, there is

really no need to accommodate the protein's charge contribution since its

concentration is effectively zero. This is the case where the effects of

the protein's net charge is least pronounced.

3) Periodic boundary conditions, this is essentially equivalent to periodic

boundary conditions used in PME. Conceptually represents a bulk solution

with a fixed (and likely relatively high) concentration of the protein. The

protein will 'see' an infinite lattice of copies of itself whose spacing is

equal to the grid box lengths along each dimension. Thus, depending on the

size of your system, it may indeed be important to accommodate a protein's

net charge if it is relatively high. So this case falls somewhere between

case one and case 2.

So long story short, if you use zero potential conditions, you most likely

would want to account for the proteins net charge... however, this setup is

rarely used outside of method validation purposes.

For periodic boundary conditions, you may or may not need to consider the

protein's net charge. This depends on how strongly charged your protein is,

and how much padding you leave between it and the boundaries of the

simulation region (again you can look up the settings for this in the

manual). Lastly, for free boundary conditions, there is likely little need

since the setup is essentially modeling an infinite dilution.

On Mon, Jul 9, 2018 at 5:44 AM, David A Case <david.case.rutgers.edu> wrote:

*> On Mon, Jul 09, 2018, 龚乾坤 wrote:
*

*> >
*

*> > Here,I have a question about MM_PBSA/GBSA.When I calculate the Ionic
*

*> > strength (parameter ISTRNG --
*

*> >
*

*> > Ionic strength (in mM) for the Poisson-Boltzmann solvent in MM_PBSA ),
*

*> > which formula should I use ?
*

*>
*

*> Please consult the wikipedia article on "Ionic Strength" (or textbooks,
*

*> etc.) Math is kind of hard to represent in an email.
*

*>
*

*> >
*

*> > And what is the formula's unit ?
*

*>
*

*> mM, as you quote above.
*

*>
*

*> ....dac
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

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Received on Mon Jul 09 2018 - 10:00:03 PDT

Date: Mon, 9 Jul 2018 09:45:13 -0700

In the case of linear solutions to the poisson boltzmann-equation, the

ionic strength term is most easily conceptualized as a perturbation of the

diagonal elements of the matrix representation of the discretization of the

differential equations being solved numerically.

For the non-linear case, the mathematics is indeed a bit too complex to be

easily represented in an email.

As for a previous question on whether or not to include protein

contribution: In PBSA this depends on your choice of boundary conditions

(see manual for appropriate flag to control this). For linear PBSA, you

have 3 choices: Zero potential boundary, Free Boundary, and Periodic

Boundary.

1) The first is probably the least helpful to you, but in essence, zero

potential boundary (also called Dirichlet boundaries in some cases) would

be akin to placing the system inside a small cavity within an infinite

conductor. Conceptually, you could think of it like carving out a nanometer

scale cube (or rectangular prism) inside a non-reactive metal block and

filling it with your system.

In this case, the protein would quite certainly be contributing and would

represent something akin to a single molecule experiment. In some sense,

the boundaries of the system act like electrostatic 'mirrors' so the

protein essentially sees its inverse charge image right at the boundary. So

this case is where the effects of the protein's charge distribution are

most pronounced

2) For Free Boundary conditions, this conceptually represents the infinite

dilution setup that Dr. Case mentioned earlier. In that case, there is

really no need to accommodate the protein's charge contribution since its

concentration is effectively zero. This is the case where the effects of

the protein's net charge is least pronounced.

3) Periodic boundary conditions, this is essentially equivalent to periodic

boundary conditions used in PME. Conceptually represents a bulk solution

with a fixed (and likely relatively high) concentration of the protein. The

protein will 'see' an infinite lattice of copies of itself whose spacing is

equal to the grid box lengths along each dimension. Thus, depending on the

size of your system, it may indeed be important to accommodate a protein's

net charge if it is relatively high. So this case falls somewhere between

case one and case 2.

So long story short, if you use zero potential conditions, you most likely

would want to account for the proteins net charge... however, this setup is

rarely used outside of method validation purposes.

For periodic boundary conditions, you may or may not need to consider the

protein's net charge. This depends on how strongly charged your protein is,

and how much padding you leave between it and the boundaries of the

simulation region (again you can look up the settings for this in the

manual). Lastly, for free boundary conditions, there is likely little need

since the setup is essentially modeling an infinite dilution.

On Mon, Jul 9, 2018 at 5:44 AM, David A Case <david.case.rutgers.edu> wrote:

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Received on Mon Jul 09 2018 - 10:00:03 PDT

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