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

David van der Spoel spoel at xray.bmc.uu.se
Thu May 3 10:16:00 CEST 2007

Mark Abraham wrote:
> Tsjerk Wassenaar wrote:
>> 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.
> Well, yes, but cutting a triclinic portion out of a triclinic crystal is 
> not an operation you'd expect a simulation package to be able to do, 
> unless it was designed primarily for crystalline simulations. It's an 
> operation from a quite different domain from standard gromacs operations.
Maybe you want to look into CCP4 programs, they can handle all kinds of 
symmetry operations etc.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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