[gmx-users] cutting out a portion of a crystal using triclinic box

[Tsjerk Wassenaar]

Hi Andrea,

On 5/3/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Andrea Robben Browning wrote:
> > I am trying to cut out a portion of a large equilbrated crystal to make
> > a smaller crystal.  I have been using the genbox command but since it
> > tries to fill up a brick of space and my crystal is triclinic I end up
> > will dangling molecules.  Is there any command that can cut a larger
> > configuration using a triclinic shape?  I also looked at using the
> > editconf command but it didn't actually cut out molecules.
>
> gromacs is designed primarily for non-crystalline simulations,

Well, I wouldn't go that far. Gromacs is designed to work with
triclinic systems. But what do you mean with 'dangling molecules'? PBC
perhaps? Chapter 3...
Please phrase your questions clearer next time...

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
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