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

[James Starlight]

by the way also I'd like to know what options for the pbc should I
specify that my system looked like infinite lattice in the x-y dims ?

James

2013/1/2, James Starlight <jmsstarlight at gmail.com>:
> Bogdan,
>
> 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 ?
>
> James
>
> 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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>