[gmx-users] micelle clustering

[Mark Abraham]

On 12/24/2011 8:01 PM, mohammad agha wrote:
> Dear GROMACS users
>
> I want to analysis of 2 micelles that are created in one simulation, 
> when I view output of trajectory by vmd or ngmx:
> ngmx -f md.trr -s md.tpr
> has been created 2 micelles, then I try to micelle clustering by:
>
>  1. |trjconv -f md.xtc -o a_cluster.gro -e 0.001 -pbc cluster|
>  2. |grompp -f md.mdp -c a_cluster.gro -o a_cluster.tpr|
>  3. |trjconv -f md.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump|
>
> but when I view cluster.xtc, just has been created one micelles and 
> remainder of monomers have been collected in different places in 3 or 
> 4 groups!!!
>
> May I know why do this occur? and where is my mistake? and what should 
> I do, please?

Hard to say, because we don't know what your objective is. You need to 
be very clear in your own mind what you want to see if the underlying 
behaviour is that the two micelles move away from each other in one cell 
and meet each other across another boundary, and design a workflow 
accordingly.

I suggest you read trjconv -h carefully and consider the workflow advice 
here 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark

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