Gromacs

Micelle Clustering

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    This is necessary for the g_spatial tool if you have a fully-formed single aggregate and want to generate the spatial distribution function for that aggregate or for solvent around that aggregate.

    Clustering to ensure that the micelle is not split across a periodic boundary condition border is an essential step prior to calculating properties such as the radius of gyration and the radial distribution function. Without this step your results will be incorrect (a sign of this error is unexplained huge fluctuations in the calculated value when the visualized trajectory looks fine).

    Three steps are required:

    1. 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.
    2. use grompp to make a new tpr file based on the frame that was output from the step above.
    3. use trjconv -pbc nojump to produce the desired trajectory using the newly produced tpr file.

    More explicitly, the same steps are:

    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
    Page last modified 10:39, 10 Oct 2009 by JLemkul?