non-polar desolvation forces

[Bruce Niessner]

Hey there,

I have a few problems understanding how to use the new non-polar desolvation forces. If I understand the documentation  on it correctly,  I have to specify "molecular_mechanics" in the tag "force_field" in the simulation file.

First question: What is the difference between spline and molecular_mechanics? (I could not find that in the docs)

Then, once I specified molecular_mechanics I can specify a parameter file. In the parameter file there are some blocks that are mandatory and others that are not.

Second question: Am I correct in the understanding that if I do not specify a file, BrownDye will just use default values?

If so? Given that the block about the desolvation forces, is there a possibility to just specifiy the parameters for the non-polar desolvation?

And is there some default parameter file, because from the documentation I don't quite understand how to specify them.

Fourth question: Is it possible to turn of the lennard jones potential and only use the non-polar desolvation forces?

Thank you very much in advance!

best Jakob

 

[Gary Huber]

Hi, Jakob,

The molecular_mechanics model uses algebraic terms that are equivalent to common molecular mechanics force fields used in MD simulations, in addition to the polar desolvation forces.

The spline model uses splines to describe the pair-wise (other than the charges), bond, bond angle, and torsion potentials.   Both force models can use APBS grids to compute electrostatic forces.

For the molecular_mechanics model, if there is no parameter file, then Browndye assumes just the repulsive 1/r^12 interaction, with the parameter chosen to approximate a hard-sphere interaction based on the atomic radius.  This can work for rigid cores, but you need to have a parameter file if you use chains.  If you don't want to use the polar solvation model (which will soon be fixed, I hope), you can just set the desolvation_parameter to zero.

For now, there is no default parameter file for the molecular_mechanics model. At some point I'll include one based on OPLS. If you could turn off the LJ forces, then the molecules would pass through each other unphysically.

If you have other questions, let me know.

Gary 

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[Bruce Niessner]

Thank you very much. That is helpful!

Do I understand it correctly then, that I can not just have a file that will only specify the parameters for the non-polar desolvation? (Maybe someone would like to change only those)

and

Can I then also infer that the overlap is only handled via the Lennard-Jones potential?

I am asking this because SDA also has an exclusion grid as well!

Thank you very much!

[Gary Huber]

Correct; we do not have a separate exclusion grid like SDA.  It's all done through the LJ forces.

Gary