[gmx-users] gmx trjconv

[Giuseppe R Del Sorbo]

Dear users,

I might need an help with gmx trjconv.


I have a system with a lysine + a micelle attached on it and I have to 
analyse the radial spherical distribution on the micelle.

The idea is to center the micelle and to work on it.

I used the command "gmx trjconv - cluster" to get a centered micelle and 
if I visualize it in vmd everything is fine.

Accordind with the manual I have to follow this three steps:


     1) trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
     2) grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr
     3) trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump

For the first two steps everything is ok, but for the last one it 
doesnt't work. Gromacs doesn't give any error, but it doesn't run.

Than I tried to write the third step without "-pbc nojump" and it works, 
but the trajectory is a mess and I can also see the lysine, when I 
should only see the micelle..

Do you have any suggestion?

Thanks a lot


Giuseppe