[gmx-users] Re: question about [ pairs ] and interaction 1-4

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> For what it's worth, I've had this experience with some molecules 
> before  with phosphatidic acid derivatives.  It seems to only happen 
> during in vacuo EM. When in the presence of solvent or bound to a 
> protein it is less of an issue since the surrounding tends to 
> out-compete intramolecular interactions.  The biggest problem is in 
> bilayers, where I've gotten around exploding molecules by setting 
> [exclusions] between the H and all phosphate O atoms.  After solvation, 
> the problems tend to go away, since the solvent can satisfy the strong 
> electrostatic interactions in these parts of the molecule.
> 

I should clarify that I remove any [exclusions] after doing EM, since solvated 
systems seem to be stable enough to not need these artificial settings.

-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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