[gmx-users] micelle clustering

[mohammad agha]

Thank you very much.

Best Regards
Sara



________________________________
 From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, December 24, 2011 1:48 PM
Subject: Re: [gmx-users] micelle clustering
 

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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