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

James Starlight jmsstarlight at gmail.com
Tue Jan 1 20:01:33 CET 2013

Have someone else any ideas how the topology for a simple 2D lattice
could be done ?:)

I've tried to build it manually but for the system of 48 nodes
definition of the angles and impropers have appeared very routinely :(


2012/12/30, James Starlight <jmsstarlight at gmail.com>:
> Hi Leandro!
> Actually I need such model of simple 2D lattice for study of the
> hessian matrix. So I'd like to perform simulation of very simple
> system without any rotation freedoms and calculate eigenvectors from
> that trajectory by means of Esential dynamics analysis. Than I'd like
> to watch on what exactly principal components different motions would
> be observed. Finally I'd like to calculate normal modes from different
> MD snapshots and compare different sub-spaces with the EDA results. So
> any aproximate system for such task would be suitable (I've decided to
> use lattice because it's most simple that I've imagine ). By the way I
> supose that such topology coupld be eaasily done from topology of
> fullerene :) But I've lack it too.
> James
> 2012/12/30 Leandro Bortot <leandro.obt at gmail.com>:
>> Leandro

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