Mark Abraham wrote:
Tsjerk Wassenaar wrote:
Hi Andrea,
On 5/3/07, Mark Abraham <[EMAIL PROTECTED]> 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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