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

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 3 00:29:31 CEST 2007

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, so I 
can't think of a reason why any of its utilities would do this. I think 
you'll have to write your own script.


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