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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu May 3 06:37:02 CEST 2007

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 A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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