Thank you very much.
Best Regards
Sara
________________________________
From: Mark Abraham <mark.abra...@anu.edu.au>
To: Discussion list for GROMACS users <gmx-users@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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