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

James Starlight jmsstarlight at gmail.com
Wed Jan 2 14:58:25 CET 2013


Thank you for explanation. Indeed the problem was in the LINCS
constrains which was not required for the lattice system.

By the way now I'd like to simulate the same 2D flexible ( in non
planar hybridization) lattice but consist of non-hydrogens atoms only
( only atoms forming lattice scaffold ). Does it possible to change
Carbon atom-valence (from 4 to 3) preventing tetragonal-like geometry
( >c- ) or should I use anothe atom type for such lattice ?


2013/1/2, Bogdan Costescu <bcostescu at gmail.com>:
> 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
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