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

James Starlight jmsstarlight at gmail.com
Wed Jan 2 15:26:29 CET 2013

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 ?


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
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list