[gmx-users] Coordinate file for lipid bilayer

Justin Lemkul jalemkul at vt.edu
Wed Oct 3 15:03:50 CEST 2012

On 10/3/12 8:59 AM, James Starlight wrote:
> Justin,
> Might the modifications of the vdwradii.dat be suitable for such
> system expanding or (on other hand) reduction (as in the below picture
> are shown). In the lattter case I defined new box dimensions (smaller
> than initial box dims) and would like to remove all side water-lipids
> layer which are beyond new pbc dimensions)?
> http://imageshack.us/content_round.php?page=done&l=img138/5497/reduction.png

I don't know if that will have much of an effect or not.  The values in 
vdwradii.dat are used to determine if there is atomic overlap with coordinates 
being added (solvent) to the solute configuration.


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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