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

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 16 02:54:17 CEST 2010

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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