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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