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

[David van der Spoel]

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.
________________________________________________________________________
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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