[gmx-users] cutting out a portion of a crystal using triclinic box
Mark.Abraham at anu.edu.au
Thu May 3 07:00:15 CEST 2007
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.
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