[gmx-users] Simulating crystalls
karamyog.singh at gmail.com
Wed May 24 17:06:52 CEST 2006
I am trying to simulate a crystal too. I have a box size of .65 nm and there
are 8 bcc crystals in the system. Lattice parameter = 0.287 nm.
I get a segmentation fault after mdrun -v. Is an atom with co-ordinates
0.574 0.000 0.000 equivalent to 0.287 0.000 0.000 in such a system? What I
am trying to ask is, does GROMACS consider these as 2 different atoms placed
at the respective positions or do the 2 atoms overlap?
What could be the reason for the segmentation fault? Is it because the atoms
are too close to each other?
On 5/23/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> David van der Spoel wrote:
> > Gale, Ella wrote:
> >> Thanks for the advice, but my force-field has no charges and hence no
> >> coulomb potential, so I want the atoms to interact with itself via the
> >> Van der Waals functions. I'm using 3.2.1 at the moment and there is no
> >> option to use any of the Ewald summation techniques. Is this something
> >> that has been added in the most recent version?
> > Ewald variant are only for Coulomb so far. You can use a normal cutoff
> > or a shifted cutoff.
> One or two of the early PME papers describe implementation details for
> LJ PME, but I am not immediately aware of a modern MD code that
> implements it. If you want it, shop around.
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