[gmx-users] Re: Simulation of 2D lattice model

[Bogdan Costescu]

On Wed, Jan 2, 2013 at 1:15 PM, James Starlight <jmsstarlight at gmail.com> wrote:
> so why my simulation of the sp3 lattice have been crashed with the
> links warnings ( which always tells about wrong geometry in topology)?

I might have missed something from the beginning of this discussion...
Why do you use LINCS with a lattice ? What do you expect to obtain ?
LINCS is normally used to keep bonds at their equilibrium length. If
you do this in a lattice, the degrees of freedom will be strongly
reduced, due to the coupled/restricted motions. How does this
influence what you want to observe ? If you are not interested in the
flexibility of the lattice itself, have you considered freezing it ?

Cheers,
Bogdan