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

[Mark Abraham]

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.

Mark