|Subject:||Re: [ESPResSo-users] Bjerrum Length for Explicit Solvent|
|Date:||Sat, 5 Oct 2013 22:07:32 -0400|
this is a beautiful example of the confusion that arises if one does not
distinguish between the physics one wants to describe and the computer
variables one types into one's favorite simulation engine.
The Bjerrum length is the distance at which the electrostatic part of the
free energy of interaction between two unit charges is equal to the thermal
energy. I concede that my previous email didn't have the important word "free"
in it. But anyways, this is how it is defined, and no computer simulation
software in the world will change that. Whether one uses implicit solvent
or explicit solvent, at the end of the day, it must be true that if you put
two unit charges at that distance into your simulation, their potential of
mean force in that solvent is equal to the thermal energy.
Now, in ESPResSo the Bjerrum length is apparently used as an input
parameter for electrostatics. That is partially convenient, but also partially
confusing. Stefan is right that if you use an implicit solvent water model,
you would type in 7 Angstrom at that point, while if you have an explicit
water model there, there is no need to account for a dielectric constant,
since it will be created explicitly by the solvent. Electrostatic interactions
then don't have a dielectric permittivity in them, and one can account that
by using a value for the Bjerrum length corresponding to vacuum, and
that is about 56nm (not Angstrom!). But that only means that the parameter
in the script is set to that value. The Bjerrum length in your simulation should
be 7A. If it is not, you are simply not simulating water. (In fact, it probably
is not, since hardly any model is perfect in giving the right dielectric constant,
and you certainly wouldn't know just by guessing it.)
I also disagree that it's impossible to measure the Bjerrum length. Of course
it is possible. All you need to do is to measure the potential of mean force
between two unit charges in your system as a function of distance, and look
for the distance where it is equal to the thermal energy. This has been done.
As Stefan suggests, you could alternatively calculate the dielectric constant
of your system and calculate the Bjerrum length from there.
So again: My main point here is: Please don't lose the physics out of sight.
It is all fair and square if your simulating day in and day out to think about
the values of your input parameters. But it is all too easy to forget that the
value of the input parameters and the physical meaning of the things they
are supposed to represent are not necessarily the same. I have witnessed
too often to count that people waste weeks of research by that. In this case:
Yes, if you want to simulate an explicit water model, you cannot set the value
of the Bjerrum length input parameter in the Espresso Script to 7 Angstrom.
And yet, that does not mean that suddenly the Bjerrum length is different.
It means that the physics is the same but the model is different, and what
is called "Bjerrum length" in the input script is no longer the Bjerrum length.
ESPResSo was developed in a time where nobody wanted to simulate
explicit water with it, and hence it was natural to call the strength parameter
of the electrostatic interaction the Bjerrum length, since people always used
implicit models. Now that explicit models are used as well, you simply have
to jury-rig the code and make it do what you want. You crank up the input
parameter of the Bjerrum length to its vacuum value. But that doesn't mean
that the value of the Bjerrum length depends on the model. The Bjerrum
length is a physics concept and must be model independent. Instead, the
input parameters of the model must be adapted such as to reflect the right
physics. Sadly, the input parameters were given physical names, and this
now may or may not cause confusion.
To be fair: Jezreel probably asked about the input parameter in the first
place. But the language was confusing. Maybe I'm just a bit too pedantic
to point all of this out, but in my experience it is helpful to keep a very clean
line between the physics one wishes to describe and how to algorithmically
implement this. Using a clear language is never a mistake.
On Oct 5, 2013, at 9:19 PM, Jezreel Castillo <address@hidden> wrote:
|[Prev in Thread]||Current Thread||[Next in Thread]|