[gmx-users] problem with trjconv -pbc cluster

jagannath mondal jmondal2004 at yahoo.co.in
Wed Jul 7 08:34:49 CEST 2010

Hi,  I had a system of surfectants which are started with an initial configuration where all of them are well dispersed. Visual study of trajectory shows they start aggregating and finally form two discrete micelles. To quantify this micelle clusterization, I tried to use the suggestions present in the gromacs documentations: http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering
i.e    use trjconv -pbc cluster to obtain a single frame that has all of the lipids in the unit cell. This must be the first frame of your trajectory. A similar frame from some previous timepoint will not work.use grompp to make a new tpr file based on the frame that was output from the step above.use trjconv -pbc nojump to produce the desired trajectory using the newly produced tpr file.trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc clustergrompp -f a.mdp -c a_cluster.gro -o a_cluster.tprtrjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump
But, The first step i.e. trjconv -pbc cluster does not work. Looks like it is going through an infinite loop and is not stopping for convergence.
I am using gromacs 4.0.7
Any help will be appreciated.

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