[gmx-users] trjconv and g_clustsize

[mohammad agha]

Dear Prof.

I have several questions about trjconv, please help me.

In my simulation is created 2 micelles.
1- When I do 3 steps of micelle clustering as follows:

  a- trjconv -f md.xtc -o a_cluster.gro-e 600000 -pbc cluster
 b- grompp -f md.mdp -c a_cluster.gro -o a_cluster.tpr
 c- trjconv -f md.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump

I view 2 micelles according to result of my simulation in VMD but in ngmx isn't view 2 micelles but just is view 1 micelle and reminder of monomers are collected in several groups in different places.
Is it right if my criterion be view in VMD and is my micelle clustering correct?


2- If I select surfactants for clustering group and system for output group in step (a) and I select system for output group in step (c), command g_clustsize doesn't work correct, consequently, I did under step and made a .xtc file only for surfactants: 

   

    i- trjconv -f md.trr -o md-surfactant.xtc -n index.ndx

    

Then I did steps a, b and c for md-surfactant.xtc and in all of steps I selected surfactants for clustering and output group. Next, I did g_clustsize and it answered me correct.   

May I know that my way is correct, please?


3- By upper way I have 2 micelles that I got index.ndx file for cluster with maximum size by g_clustsize (maxcluster.ndx).
May I know how can I use from this for next calculation if I want consider only maximum cluster with all of system (water and ion) in calculations (for example rdf, gyration and etc)?


Please help me

Best Regards 

Sara
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