[gmx-users] micelle clustering

[mohammad agha]

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?
Please help me.

Best Regards
Sara  
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